The filovirus family includes viruses such as Ebola, Marburg, and Sudan viruses that can cause hemorrhagic fever and severe disease (Feldmann et al., 2013). Filoviruses package their single-stranded negative-sense RNA genomes with viral proteins including nucleoprotein (NP), VP24 and VP35, into helical ribonucleoprotein assemblies called nucleocapsids (NCs) (Huang et al., 2002; Noda et al., 2010; Wan et al., 2017). NCs are recruited to the plasma membrane and bud from the host cells as enveloped virions with a characteristic filamentous morphology from which the family takes its name (Geisbert and Jahrling, 1995).

The filovirus matrix protein, VP40, binds to and concentrates at the plasma membrane of infected cells, where it can interact with components of the NC to promote envelopment, and where it drives formation of the filamentous virus particles. VP40 is required for viral budding, and expression of VP40 alone is sufficient to drive formation of filamentous virus-like particles (VLPs) containing a matrix layer and membrane envelope (Harty et al., 2000; Jasenosky et al., 2001; Noda et al., 2002; Timmins et al., 2001). The morphology of these VLPs is similar to that of true virions but their diameter is smaller (Noda et al., 2002). When VP40 is co-expressed with NC components NP, VP24 and VP35, VLPs are produced which are almost indistinguishable from true virions (Bharat et al., 2012; Noda et al., 2005; Wan et al., 2017).

A number of crystal structures have been determined of Ebola virus VP40 (eVP40) and Sudan (Ebola) virus (sVP40) (Bornholdt et al., 2013; Clifton et al., 2015; Dessen et al., 2000; Gomis-Rüth et al., 2003). VP40 contains an N-terminal domain (NTD) and a C-terminal domain (CTD), linked by an intrasubunit hinge. Both eVP40 and sVP40 have been crystallized in space group C2 with similar unit cell dimensions. These crystals reveal dimers assembled via a hydrophobic interface in the NTD, involving residues A55, H61, F108, A113, M116, and L117 which are distributed across two alpha-helices (residues 52–65, 108–117). Disruption of the NTD dimer interface by site-directed mutagenesis prevents migration of VP40 to the plasma membrane and prevents matrix assembly (Bornholdt et al., 2013). Within the typical C2 crystal packing of unmodified VP40, eVP40, and sVP40 dimers are further arranged in linear assemblies via a hydrophobic CTD-CTD interface (Bornholdt et al., 2013; Dessen et al., 2000; Figure 1—figure supplement 1A,B). This interface involves residues L203, I237, M241, M305, and I307, which together form a relatively smooth hydrophobic patch (Figure 1—figure supplement 1A). The CTD also contains a basic patch composed of six lysine residues (K221, K224, K225, K270,K274, K275), which is essential for matrix assembly and membrane budding (Figure 1—figure supplement 1A).

A crystal structure of Marburg VP40 (mVP40) has also been determined (Oda et al., 2016; Figure 1—figure supplement 1C). eVP40 and mVP40 have 42% sequence identity and a C-alpha RMSD of 2.4 Å in the NTD, but only 16% sequence identity and 5.6 Å C-alpha RMSD in the CTD. The overall topology of mVP40, however, is similar to that of eVP40. The mVP40 monomer has similar N- and C-terminal domains, although there is a small rotation of the CTD relative to the NTD when compared to eVP40. mVP40 dimerizes via an NTD interface that is very similar to that in eVP40, and mVP40 also forms dimers in solution that are required for membrane binding and filament budding. The mVP40 CTD basic patch is also required for membrane binding but is larger and flatter than that in eVP40. In the mVP40 crystal packing, the CTDs meet at an angle and do not form the more extensive hydrophobic interface observed in the C2 crystals of eVP40 and sVP40 (Figure 1—figure supplement 1).

Deletion or proteolysis of the C-terminus or C-terminal domain or incubation with urea drives oligomerization of the eVP40 NTD into RNA-binding octameric rings (Bornholdt et al., 2013; Gomis-Rüth et al., 2003). Subsequent work suggests that octameric rings are likely to have a function during the viral lifecycle independent of matrix formation (Bornholdt et al., 2013; Gomis-Rüth et al., 2003; Hoenen et al., 2005; Hoenen et al., 2010b).

In an effort to mimic membrane-associated electrostatic conditions, a crystal structure of eVP40 was determined in the presence of the negatively charged additive dextran sulfate (Bornholdt et al., 2013). Under these conditions, eVP40 assembled into linear hexamers (Figure 1—figure supplement 1D) with unit distances approximately consistent with earlier, lower resolution tomographic analysis of the VP40 layer in Ebola and Marburg virions (Beniac et al., 2012; Bharat et al., 2011). The core of the linear hexamer consists of four NTDs from which the linked CTDs are disordered or ‘sprung’ and not resolved. The first and sixth VP40s in the hexamer retain their CTD in close association with its NTD. These CTDs assemble into linear filaments via the same CTD-CTD interactions observed in the C2 crystals of VP40 dimers. The NTD-NTD interfaces within the hexamer alternate between the dimer interface and the same NTD-NTD interface observed in the octameric ring. No linear hexamer structure has been determined for mVP40. However, mutagenesis of residues in mVP40 homologous to those forming the ‘octamer-like’ interfaces in hexameric eVP40 (Bornholdt et al., 2013; Hoenen et al., 2010a) retains the ability of mVP40 to dimerize but prevents membrane binding and budding. Based on existing data it seems likely that VP40 is arranged in a similar way in both MARV and EBOV particles.

The current model for the assembly state of VP40 within filovirus particles consists of VP40 hexamers as crystallized in the presence of dextran sulfate, arranged to form a 2D lattice, with dimensions of the 2D lattices in the model based upon repeating features observed in low-resolution cryo-electron tomography (cryo-ET) studies (Beniac et al., 2012; Bharat et al., 2011; Bornholdt et al., 2013). Analysis of transfected cells suggested that VP40 assembles into hexamers and octamers at the plasma membrane and in protrusions (Adu-Gyamfi et al., 2012) and that the interaction is mediated by the C-terminal domains (Adu-Gyamfi et al., 2013). The structure and arrangement of VP40 within actual assembled virus particles, however, is unknown. It therefore remains unclear how VP40 assembles in the actual virion, which model of VP40 assembly best reflects that in the virion, and how VP40 induces membrane curvature and assembly with other viral components. Here, we have set out to directly determine the structure and arrangement of VP40 within filamentous virus-like particles and authentic filovirus virions.

The linear CTD-CTD interface is consistently observed in unmodified VP40 crystals eVP40 and sVP40, with intact CTDs and in the absence of charged additives, consistently crystallize in linear filaments of dimers in the space group C2 (Bornholdt et al., 2013; Clifton et al., 2015; Dessen et al., 2000). In an attempt to determine if this linear arrangement is an inherent preferred assembly interface of eVP40 or simply the result of the common C2 crystal packing, we crystallized eVP40 in two alternate crystal forms: P6₂ and P6₄22. Notably, in both of these crystal forms, eVP40 also builds linear filaments of dimers, mediated by CTD-CTD interdimer interfaces, with CTD basic patches displayed on a common face. These filaments differ from the C2 filaments by slight torsional rotation about the relatively flat hydrophobic CTD-CTD interface (Figure 1—figure supplement 1E,F and Table 1). The propensity of VP40 to form linear assemblies by CTD-CTD interactions across multiple crystal forms suggest this is a biologically preferred interface and may be important in the viral particle or virus assembly.

The structure of the matrix layer in EBOV VLPs eVP40 expression induces budding of long VLPs from the surface of mammalian cells (Noda et al., 2002; Timmins et al., 2001). We purified Zaire eVP40 VLPs by sucrose gradient purification and imaged them by cryo-ET, finding multi-micron long filaments with a diameter of ~ 28 nm (Table 2) and a matrix-like protein layer visible under the membrane bilayer. We applied subtomogram averaging methods to determine the structure of the matrix layer to a resolution of 10 Å (Figure 1, Figure 1—figure supplement 2) from intact eVP40 VLPs. We observed that the matrix layer is formed by higher-order linear oligomerization of VP40 dimers on the inner surface of the viral membrane. VP40 dimers form long chains that stack to form 2D lattices with a monoclinic p2 space group in the plane of the membrane (Figure 1, Table 2). The crystal structure of the C2 eVP40 dimer (PDB: 4LDB) could be fit as a rigid body into the density, showing that linear oligomerization is mediated by CTD to CTD interactions.

Figure 1 with 4 supplements see all

Download asset Open asset

In addition to eVP40 VLPs, we also produced VLPs by co-expression of eVP40 with the Ebola virus glycoprotein GP, and by co-expression of eVP40 with the NC components NP, VP24 and VP35. As described previously (Bharat et al., 2012), NP-VP24-VP35-VP40 VLPs have substantially wider filaments to accommodate the NC-like assembly (Table 2). We determined the structures of eVP40 within these VLPs at resolutions of 10 Å, (Figure 1, Figure 1—figure supplement 2). As in the eVP40 VLPs, the matrix layer in these VLPs is formed from extended chains of eVP40 that stack to form monoclinic p2 lattices (Figure 1, Table 2).

The structure of the matrix layer in MARV

In order to determine if the disparate sequence of the MARV VP40 CTD still resulted in a matrix assembly similar to that of eVP40, we prepared and purified mVP40 VLPs and determined the structure of the matrix layers to 10 Å resolution (Figure 2, Figure 2—figure supplement 1). The matrix layer appears similar to that seen in eVP40 VLPs, adopting a p2 lattice with similar dimensions (Figures 1 and 2), suggesting that the structure is conserved despite sequence divergence (34% identical, 49% homologous). We fit the dimeric mVP40 crystal structure as well as a dimeric eVP40 crystal structure into the density as a rigid body. For mVP40, there were clashes of the CTDs at the inter-dimer interface (Figure 2—figure supplement 2), while eVP40 fit these densities well. This suggests to us that the CTD of mVP40 is rotated slightly about the CTD-NTD hinge into a position more similar to that of eVP40 when assembled in VP40 VLPs. A structural change in mVP40 in membrane binding has been proposed in prior simulation studies (Bhattarai et al., 2017).

Figure 2 with 2 supplements see all

Download asset Open asset

We generated authentic MARV virions by infection of Huh7 cells and imaged fixed, purified virions by cryo-ET. MARV virion matrix layers again consist of VP40 dimers forming extended chains through their CTDs and stacking of these chains form a 2D p2 lattice (Figure 2), but the lattice angles differ from those in VLPs: the VP40 chains run nearly perpendicular to the filament axis, and the register of neighboring chains differs by approximately half a VP40 protomer from those seen in VLPs (Figures 1 and 2). Rigid body fitting of mVP40 dimers or eVP40 dimers shows a good fit with no extra, unassigned densities (Figure 2), suggesting that VP40 is the only component in the matrix layer. At this resolution we are unable to confidently assess whether the CTD has rotated slightly relative to the NTD or not.

We attempted to determine the structure of the matrix layer within authentic, fixed Ebola virions, but found that some membranes were ‘moth-eaten’, leaving membrane and matrix layers disrupted, while in others there were only few places where an ordered matrix layer was observed (Figure 3—figure supplement 1). We were therefore unable to determine a structure for VP40 within authentic EBOV virions.

Global order of filovirus matrices

Lines of density that correspond to VP40 dimer chains are directly visible in tomograms of VLPs and viruses (Figure 3A). General features such as the orientation of the chains relative to the axis of the filamentous particle are consistent with those determined by subtomogram averages.

Figure 3 with 1 supplement see all

Download asset Open asset

When determining structures, subtomogram averaging provides the position and orientation of each VP40 dimer-centered subtomogram within the tomogram. Visualizations of these positions and orientations are called ‘lattice maps’ and reveal the global arrangement of VP40 (Figure 3B,C). Lattice maps show that in all VLPs studied, 2D lattices form locally ordered patches, and that there are disordered areas or other defects in crystallographic packing between the patches. The local pitch of the array is somewhat variable, and VP40 chains can terminate and run into each other. The overall topology of the matrix layer is a ‘patchwork’ of locally ordered 2D lattices.

Based on the relative positions of subtomograms as visualized in the lattice maps, we calculated and plotted the average radius for each filamentous particle (at the matrix layer) against the pitch angle of the VP40 chains relative to the circumference of the VLP (Figure 4). We find that despite the large differences in radius and angle, the radius of curvature of the VP40 chains is similar in all VLPs. Because we had not determined the structure, we did not derive these parameters for Ebola virions. Nevertheless, where small ordered regions of VP40, or isolated VP40 chains were observed, they had a variable, but small angle relative to the filament, suggesting they have a radius of curvature similar to that observed in NP-VP24-VP35-VP40 VLPs (Figure 3—figure supplement 1).

Figure 4

Download asset Open asset

Spatial relationships between EBOV VP40 and other viral proteins

We next analyzed the spatial relationship between eVP40 and the other viral components NC or GP. To do this, we first required the positions and orientations of the other viral components. For EBOV NP-VP24-VP35-VP40, NC positions had been calculated previously while determining the structure of the NC (Wan et al., 2017). For EBOV VP40-GP VLPs, we determined a low-resolution structure of Ebola GP, thereby determining its position (Figure 5—figure supplement 1). We then generated neighbor density maps: these show the relative distribution of all subtomograms of interest (those containing GP or NC) with respect to all reference subtomograms (those containing VP40) (Figure 5).

Figure 5 with 1 supplement see all

Download asset Open asset

We found that the NC layer is positioned at a consistent radial distance from VP40, but otherwise shows no defined spatial relationships with VP40 particles (Figure 5). This arrangement is consistent with the presence of a tether (likely contributed by NP) that radially links VP40 and the NC layer. We estimated the stoichiometric ratio between VP40 and NC as ~ 4.4, suggesting that only a minority of VP40 molecules can be simultaneously bound by such a tether, and explaining the absence of any density corresponding to a bound tether in our VP40 structure.

We found that GP does not form an ordered lattice on the membrane. There is, however, a consistent radial distance between VP40 and nearby GP (Figure 5); this distance is related to the thickness of the membrane envelope as is expected for proteins bound on opposite sides of the envelope. A tangential view of the neighbor plot shows weak striations in the GP layer, suggesting a tendency for GP to sit in preferred positions relative to the underlying VP40. We radially projected the GP neighbor positions onto the underlying VP40 lattice, revealing that GP is preferentially located at positions near the CTD-CTD interfaces of VP40.

VP40 has been observed to adopt a number of different oligomeric states, including dimers, hexamers, octameric rings, and higher-order oligomers, which involve distinct conformations and assembly surfaces. Dimers are formed via interactions between VP40 NTDs, and represent the basic solubilized conformation of VP40 (Bornholdt et al., 2013). Octameric rings are formed using a different set of NTD-NTD interactions and appear to serve an essential RNA-binding function in a different stage of the viral life cycle distinct from its primary role as a matrix protein (Gomis-Rüth et al., 2003; Hoenen et al., 2005; Bornholdt et al., 2013), and a range of oligomers has been observed at the plasma membrane of infected cells (Adu-Gyamfi et al., 2012).

The previous model for the arrangement of VP40 within filoviruses was based upon a crystal structure obtained in the presence of dextran sulfate in which VP40 forms a hexamer. In this conformation, 6 VP40 NTDs form a linear oligomer, bracketed by a CTD on each end, with central CTDs ‘sprung’ and therefore disordered on each side of the linear core (Figure 1—figure supplement 1). In this model, the sprung CTDs protruding from one side of the NTD hexamer bind NC while those on the other side bind the plasma membrane. Higher order oligomerization of hexamers via CTD interactions were then proposed to form a matrix lattice with dimensions similar to repeating features observed in cryo-electron tomograms (Bornholdt et al., 2013).

The VP40 matrix structures observed here in VLPs and virions reveal a linear arrangement of VP40 dimers without sprung CTDs. We suggest that the assembly of the half-sprung hexamer could have been the result of crystal packing and/or the presence of dextran sulfate. The interactions of the central VP40s in the hexamer are similar to those seen in nucleic-acid-binding octameric VP40 rings. It is possible that dextran sulfate is not acting as a membrane mimic, but instead as a nucleic acid mimic and inducing a conformation related to nucleic-acid binding octameric VP40 rings. We therefore conclude that dimers and higher order oligomers of dimers, are the oligomeric states that play a role during virus assembly.

In all VP40 containing VLPs we studied, as well as in authentic MARV virions, the matrix layer is composed of linear chains of VP40 dimers, in which the dimeric interface is provided by the NTD, and the inter-dimer interface by the CTD. This linear arrangement of dimers is more similar to the packing of VP40 within C2 crystals and the P6₂ and P6₄22 crystals presented here. In this arrangement, VP40 interacts with the membrane via basic patches in the CTD. VP40 chains are stacked to form 2D lattices on the underside of the viral membrane (Figure 6).

Figure 6

Download asset Open asset

The arrangement of VP40 which we observe provides a structural explanation for the phenotypes of a number of previously characterized EBOV and MARV VP40 mutants. Mutations in the basic patch which mediates the interaction between VP40 and the membrane, inhibit membrane binding, matrix assembly and budding for both eVP40 (Bornholdt et al., 2013) and mVP40 (Koehler et al., 2018). Mutations that disrupt the NTD-NTD dimeric interface prevent membrane binding, assembly, and budding for both eVP40 (Bornholdt et al., 2013; Oda et al., 2016) and mVP40 (Koehler et al., 2018), consistent with the key role of this interface in higher-order oligomerization of VP40. Mutations such as eVP40-M241R, which disrupts the hydrophobic patch of the CTD-CTD interface, lead to crystal forms which poorly recapitulate the CTD-CTD interface, while expression of eVP40 M241R or I307R block matrix assembly and budding (Bornholdt et al., 2013). Introduction of M305F/I307F instead of I307R, to enhance the hydrophobic interface, also enhances proportion of VLP release relative to expression level. Both mutants are consistent with a role for linear oligomerization of VP40 dimers via the hydrophobic CTD interface in promoting membrane curvature and filament growth (Bornholdt et al., 2013). Complete disruption of the CTD-CTD interface (eVP40-R134A/I307R) allows for membrane binding but not oligomerization, and neither budding nor ruffling is observed (Bornholdt et al., 2013). Other mutations to the CTD further disrupt membrane interactions and assembly (Adu-Gyamfi et al., 2013).

The matrix layer we observe in both VLPs and in MARV virions has only local order. Patches of ordered VP40 are separated by various defects in the 2D crystallographic packing. It has been suggested that VP40 VLPs elongate perpendicularly from the plasma membrane (Kolesnikova et al., 2007b; Kolesnikova et al., 2007a). While it is possible to envisage filament protrusion as mediated by highly processive extension of VP40 chains at the base of an extending filament, our data are more consistent with assembly of the VP40 lattice from multiple starting points to generate a patchwork of locally ordered lattices at the assembly site. This mode of assembly is also easier to reconcile with our previous data suggesting that the budding of virions containing an NC takes place like a surfacing submarine, where the NC initially protrudes parallel to the membrane surface before being wrapped from one end (Welsch et al., 2010). Because VP40 chains adopt preferred curvatures and therefore are oriented in a defined orientation relative to the membrane, neighboring patches would tend to agglomerate with their VP40 chains in approximately the same orientation.

We were unable to determine the structure of VP40 in Ebola virions, as the majority of viruses showed unstructured matrix layers. We think this is likely a fixation artefact, as Ebola virus preparations were generally more delicate than Marburg virus preparations. However, given our results with VLPs and the observations of ordered patches in some Ebola virions, we suggest that VP40 forms patchwork lattices of the same structure in Ebola virus.

We do not observe any substantial contribution to matrix density from another protein. However, given the ~ 4.4 VP40:NP ratio which we observed, we cannot rule out that a small part of every NP binds to one VP40 molecule, since the sub-stoichiometric levels of binding of a small additional density might not be detected.

GP has been previously shown to migrate toward VP40-rich membrane areas and colocalize with VP40 in VLPs (Licata et al., 2004; Noda et al., 2002). We observed that in EBOV VP40-GP VLPs, GP has a tendency to locate to striations that run perpendicular to the VP40 chains. These data suggest that GP preferentially sits at positions close to the inter-dimer CTD-CTD interfaces. Such a preferential localization could be derived through a direct interaction between VP40 CTD and the short, five-residue cytoplasmic tail of GP. Alternatively, VP40 CTD may modify the local lipid composition to generate a local environment favorable to the GP trans-membrane domain.

Our data reveal the arrangement of VP40 in assembled filovirus particles. They are consistent with a model for filovirus assembly in which VP40 dimers in solution migrate toward the plasma membrane, where they oligomerize into curved chains via CTD-CTD interactions, which induces local membrane curvature. Stacking of VP40 chains results in the formation of 2D lattices which are curved in one direction. Membrane curvature can be propagated over larger areas of the membrane by growth of patches of 2D lattice or by contact and ‘fusion’ between neighboring patches.

EM maps of VP40 from Ebola NP-VP24-VP35-VP40, VP40, VP40-GP VLPs and Marburg virions and VP40 VLPs were deposited in the EMDB with accession numbers EMD-11660, EMD-11661, EMD-11662, EMD-11663, EMD-11664, respectively. EM map of Ebola GP was deposited as EMD-11665. Crystal structures of eVP40 P62 and eVP40 P6422 were deposited to the PDB with accession numbers 7JZJ and 7JZT, respectively.

1. 1. Wan W
   2. Clarke M
   3. Norris M
   4. Kolesnikova L
   5. Koehler A
   6. Bornholdt ZA
   7. Becker S
   8. Saphire EO
   9. Briggs JAG

   (2020) RCSB Protein Data Bank

   ID 7JZJ. Crystal structures of eVP40 P62.

   https://www.rcsb.org/structure/7JZJ
2. 1. Wan W
   2. Clarke M
   3. Norris M
   4. Kolesnikova L
   5. Koehler A
   6. Bornholdt ZA
   7. Becker S
   8. Saphire EO
   9. Briggs JAG

   (2020) RCSB Protein Data Bank

   ID 7JZT. Crystal structures of eVP40 P6422.

   https://www.rcsb.org/structure/7JZT
3. 1. Wan W
   2. Clarke M
   3. Norris M
   4. Kolesnikova L
   5. Koehler A
   6. Bornholdt ZA
   7. Becker S
   8. Saphire EO
   9. Briggs JAG

   (2020) Electron Microscopy Data Bank

   ID EMD-11660. EM map of VP40 from Ebola NP-VP24-VP35-VP40.

   http://www.ebi.ac.uk/pdbe/entry/emdb/EMD-11660
4. 1. Wan W
   2. Clarke M
   3. Norris M
   4. Kolesnikova L
   5. Koehler A
   6. Bornholdt ZA
   7. Becker S
   8. Saphire EO
   9. Briggs JAG

   (2020) Electron Microscopy Data Bank

   ID EMD-11661. EM map from VP40.

   http://www.ebi.ac.uk/pdbe/entry/emdb/EMD-11661
5. 1. Wan W
   2. Clarke M
   3. Norris M
   4. Kolesnikova L
   5. Koehler A
   6. Bornholdt ZA
   7. Becker S
   8. Saphire EO
   9. Briggs JAG

   (2020) Electron Microscopy Data Bank

   ID EMD-11662. EM map from VP40-GP VLP.

   http://www.ebi.ac.uk/pdbe/entry/emdb/EMD-11662
6. 1. Wan W
   2. Clarke M
   3. Norris M
   4. Kolesnikova L
   5. Koehler A
   6. Bornholdt ZA
   7. Becker S
   8. Saphire EO
   9. Briggs JAG

   (2020) Electron Microscopy Data Bank

   ID EMD-11663. EM map from Marburg virions.

   http://www.ebi.ac.uk/pdbe/entry/emdb/EMD-11663
7. 1. Wan W
   2. Clarke M
   3. Norris M
   4. Kolesnikova L
   5. Koehler A
   6. Bornholdt ZA
   7. Becker S
   8. Saphire EO
   9. Briggs JAG

   (2020) Electron Microscopy Data Bank

   ID EMD-11664. EM map from VP40 VLPs.

   http://www.ebi.ac.uk/pdbe/entry/emdb/EMD-11664
8. 1. Wan W
   2. Clarke M
   3. Norris M
   4. Kolesnikova L
   5. Koehler A
   6. Bornholdt ZA
   7. Becker S
   8. Saphire EO
   9. Briggs JAG

   (2020) Electron Microscopy Data Bank

   ID EMD-11665. EM map of Ebola GP.

   http://www.ebi.ac.uk/pdbe/entry/emdb/EMD-11665

1. 1. Adams PD
   2. Afonine PV
   3. Bunkóczi G
   4. Chen VB
   5. Davis IW
   6. Echols N
   7. Headd JJ
   8. Hung LW
   9. Kapral GJ
   10. Grosse-Kunstleve RW
   11. McCoy AJ
   12. Moriarty NW
   13. Oeffner R
   14. Read RJ
   15. Richardson DC
   16. Richardson JS
   17. Terwilliger TC
   18. Zwart PH

   (2010) PHENIX: a comprehensive Python-based system for macromolecular structure solution

   Acta Crystallographica Section D Biological Crystallography 66:213–221.

   https://doi.org/10.1107/S0907444909052925

   • PubMed
   • Google Scholar
2. 1. Adu-Gyamfi E
   2. Digman MA
   3. Gratton E
   4. Stahelin RV

   (2012) Investigation of ebola VP40 assembly and oligomerization in live cells using number and brightness analysis

   Biophysical Journal 102:2517–2525.

   https://doi.org/10.1016/j.bpj.2012.04.022

   • PubMed
   • Google Scholar
3. 1. Adu-Gyamfi E
   2. Soni SP
   3. Xue Y
   4. Digman MA
   5. Gratton E
   6. Stahelin RV

   (2013) The ebola virus matrix protein penetrates into the plasma membrane: a key step in viral protein 40 (VP40) oligomerization and viral egress

   The Journal of Biological Chemistry 288:5779–5789.

   https://doi.org/10.1074/jbc.M112.443960

   • PubMed
   • Google Scholar
4. 1. Beniac DR
   2. Melito PL
   3. Devarennes SL
   4. Hiebert SL
   5. Rabb MJ
   6. Lamboo LL
   7. Jones SM
   8. Booth TF

   (2012) The organisation of ebola virus reveals a capacity for extensive, modular polyploidy

   PLOS ONE 7:e29608.

   https://doi.org/10.1371/journal.pone.0029608

   • PubMed
   • Google Scholar
5. 1. Bharat TA
   2. Riches JD
   3. Kolesnikova L
   4. Welsch S
   5. Krähling V
   6. Davey N
   7. Parsy ML
   8. Becker S
   9. Briggs JA

   (2011) Cryo-electron tomography of marburg virus particles and their morphogenesis within infected cells

   PLOS Biology 9:e1001196.

   https://doi.org/10.1371/journal.pbio.1001196

   • PubMed
   • Google Scholar
6. 1. Bharat TA
   2. Noda T
   3. Riches JD
   4. Kraehling V
   5. Kolesnikova L
   6. Becker S
   7. Kawaoka Y
   8. Briggs JA

   (2012) Structural dissection of ebola virus and its assembly determinants using cryo-electron tomography

   PNAS 109:4275–4280.

   https://doi.org/10.1073/pnas.1120453109

   • PubMed
   • Google Scholar
7. 1. Bhattarai N
   2. Gc JB
   3. Gerstman BS
   4. Stahelin RV
   5. Chapagain PP

   (2017) Plasma membrane association facilitates conformational changes in the marburg virus protein VP40 dimer

   RSC Advances 7:22741–22748.

   https://doi.org/10.1039/C7RA02940C

   • PubMed
   • Google Scholar
8. 1. Bornholdt ZA
   2. Noda T
   3. Abelson DM
   4. Halfmann P
   5. Wood MR
   6. Kawaoka Y
   7. Saphire EO

   (2013) Structural rearrangement of ebola virus VP40 begets multiple functions in the virus life cycle

   Cell 154:763–774.

   https://doi.org/10.1016/j.cell.2013.07.015

   • PubMed
   • Google Scholar
9. 1. Castaño-Díez D
   2. Kudryashev M
   3. Arheit M
   4. Stahlberg H

   (2012) Dynamo: a flexible, user-friendly development tool for subtomogram averaging of cryo-EM data in high-performance computing environments

   Journal of Structural Biology 178:139–151.

   https://doi.org/10.1016/j.jsb.2011.12.017

   • Google Scholar
10. 1. Chen S
    2. McMullan G
    3. Faruqi AR
    4. Murshudov GN
    5. Short JM
    6. Scheres SH
    7. Henderson R

    (2013) High-resolution noise substitution to measure overfitting and validate resolution in 3D structure determination by single particle electron cryomicroscopy

    Ultramicroscopy 135:24–35.

    https://doi.org/10.1016/j.ultramic.2013.06.004

    • PubMed
    • Google Scholar
11. 1. Clifton MC
    2. Bruhn JF
    3. Atkins K
    4. Webb TL
    5. Baydo RO
    6. Raymond A
    7. Lorimer DD
    8. Edwards TE
    9. Myler PJ
    10. Saphire EO

    (2015) High-resolution crystal structure of dimeric VP40 from Sudan ebolavirus

    Journal of Infectious Diseases 212:S167–S171.

    https://doi.org/10.1093/infdis/jiv090

    • PubMed
    • Google Scholar
12. 1. Dessen A
    2. Volchkov V
    3. Dolnik O
    4. Klenk HD
    5. Weissenhorn W

    (2000) Crystal structure of the matrix protein VP40 from ebola virus

    The EMBO Journal 19:4228–4236.

    https://doi.org/10.1093/emboj/19.16.4228

    • PubMed
    • Google Scholar
13. 1. Emsley P
    2. Lohkamp B
    3. Scott WG
    4. Cowtan K

    (2010) Features and development of coot

    Acta Crystallographica. Section D, Biological Crystallography 66:486–501.

    https://doi.org/10.1107/S0907444910007493

    • PubMed
    • Google Scholar
14. Book

    1. Feldmann H
    2. Sanchez A
    3. Geisbert TW

    (2013)

    Filoviridae: Marburg and Ebola viruses

    In: Knipe DM, editors. Fields Virology (Sixth Edition). Philadelphia: Lippincott: Williams & Wilkins. pp. 923–956.

    • Google Scholar
15. 1. Förster F
    2. Medalia O
    3. Zauberman N
    4. Baumeister W
    5. Fass D

    (2005) Retrovirus envelope protein complex structure in situ studied by cryo-electron tomography

    PNAS 102:4729–4734.

    https://doi.org/10.1073/pnas.0409178102

    • PubMed
    • Google Scholar
16. 1. Geisbert TW
    2. Jahrling PB

    (1995) Differentiation of filoviruses by electron microscopy

    Virus Research 39:129–150.

    https://doi.org/10.1016/0168-1702(95)00080-1

    • PubMed
    • Google Scholar
17. 1. Gomis-Rüth FX
    2. Dessen A
    3. Timmins J
    4. Bracher A
    5. Kolesnikowa L
    6. Becker S
    7. Klenk HD
    8. Weissenhorn W

    (2003) The matrix protein VP40 from ebola virus octamerizes into pore-like structures with specific RNA binding properties

    Structure 11:423–433.

    https://doi.org/10.1016/S0969-2126(03)00050-9

    • PubMed
    • Google Scholar
18. 1. Hagen WJH
    2. Wan W
    3. Briggs JAG

    (2017) Implementation of a cryo-electron tomography tilt-scheme optimized for high resolution subtomogram averaging

    Journal of Structural Biology 197:191–198.

    https://doi.org/10.1016/j.jsb.2016.06.007

    • PubMed
    • Google Scholar
19. 1. Harty RN
    2. Brown ME
    3. Wang G
    4. Huibregtse J
    5. Hayes FP

    (2000) A PPxY motif within the VP40 protein of ebola virus interacts physically and functionally with a ubiquitin ligase: implications for Filovirus budding

    PNAS 97:13871–13876.

    https://doi.org/10.1073/pnas.250277297

    • PubMed
    • Google Scholar
20. 1. Hoenen T
    2. Volchkov V
    3. Kolesnikova L
    4. Mittler E
    5. Timmins J
    6. Ottmann M
    7. Reynard O
    8. Becker S
    9. Weissenhorn W

    (2005) VP40 octamers are essential for ebola virus replication

    Journal of Virology 79:1898–1905.

    https://doi.org/10.1128/JVI.79.3.1898-1905.2005

    • PubMed
    • Google Scholar
21. 1. Hoenen T
    2. Groseth A
    3. Kolesnikova L
    4. Theriault S
    5. Ebihara H
    6. Hartlieb B
    7. Bamberg S
    8. Feldmann H
    9. Ströher U
    10. Becker S

    (2006) Infection of naive target cells with virus-like particles: implications for the function of ebola virus VP24

    Journal of Virology 80:7260–7264.

    https://doi.org/10.1128/JVI.00051-06

    • PubMed
    • Google Scholar
22. 1. Hoenen T
    2. Biedenkopf N
    3. Zielecki F
    4. Jung S
    5. Groseth A
    6. Feldmann H
    7. Becker S

    (2010a) Oligomerization of ebola virus VP40 is essential for particle morphogenesis and regulation of viral transcription

    Journal of Virology 84:7053–7063.

    https://doi.org/10.1128/JVI.00737-10

    • PubMed
    • Google Scholar
23. 1. Hoenen T
    2. Jung S
    3. Herwig A
    4. Groseth A
    5. Becker S

    (2010b) Both matrix proteins of ebola virus contribute to the regulation of viral genome replication and transcription

    Virology 403:56–66.

    https://doi.org/10.1016/j.virol.2010.04.002

    • PubMed
    • Google Scholar
24. 1. Huang Y
    2. Xu L
    3. Sun Y
    4. Nabel GJ

    (2002) The assembly of ebola virus nucleocapsid requires virion-associated proteins 35 and 24 and posttranslational modification of nucleoprotein

    Molecular Cell 10:307–316.

    https://doi.org/10.1016/S1097-2765(02)00588-9

    • PubMed
    • Google Scholar
25. 1. Jasenosky LD
    2. Neumann G
    3. Lukashevich I
    4. Kawaoka Y

    (2001) Ebola virus VP40-induced particle formation and association with the lipid bilayer

    Journal of Virology 75:5205–5214.

    https://doi.org/10.1128/JVI.75.11.5205-5214.2001

    • PubMed
    • Google Scholar
26. 1. Koehler A
    2. Pfeiffer S
    3. Kolesnikova L
    4. Becker S

    (2018) Analysis of the multifunctionality of marburg virus VP40

    Journal of General Virology 99:1614–1620.

    https://doi.org/10.1099/jgv.0.001169

    • PubMed
    • Google Scholar
27. 1. Kolesnikova L
    2. Bohil AB
    3. Cheney RE
    4. Becker S

    (2007a) Budding of Marburgvirus is associated with filopodia

    Cellular Microbiology 9:939–951.

    https://doi.org/10.1111/j.1462-5822.2006.00842.x

    • PubMed
    • Google Scholar
28. 1. Kolesnikova L
    2. Ryabchikova E
    3. Shestopalov A
    4. Becker S

    (2007b) Basolateral budding of marburg virus: vp40 retargets viral glycoprotein GP to the basolateral surface

    The Journal of Infectious Diseases 196:S232–S236.

    https://doi.org/10.1086/520584

    • PubMed
    • Google Scholar
29. 1. Kremer JR
    2. Mastronarde DN
    3. McIntosh JR

    (1996) Computer visualization of three-dimensional image data using IMOD

    Journal of Structural Biology 116:71–76.

    https://doi.org/10.1006/jsbi.1996.0013

    • PubMed
    • Google Scholar
30. 1. Li X
    2. Mooney P
    3. Zheng S
    4. Booth CR
    5. Braunfeld MB
    6. Gubbens S
    7. Agard DA
    8. Cheng Y

    (2013) Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM

    Nature Methods 10:584–590.

    https://doi.org/10.1038/nmeth.2472

    • Google Scholar
31. 1. Licata JM
    2. Johnson RF
    3. Han Z
    4. Harty RN

    (2004) Contribution of ebola virus glycoprotein, Nucleoprotein, and VP24 to budding of VP40 virus-like particles

    Journal of Virology 78:7344–7351.

    https://doi.org/10.1128/JVI.78.14.7344-7351.2004

    • PubMed
    • Google Scholar
32. 1. Mastronarde DN

    (2005) Automated electron microscope tomography using robust prediction of specimen movements

    Journal of Structural Biology 152:36–51.

    https://doi.org/10.1016/j.jsb.2005.07.007

    • PubMed
    • Google Scholar
33. 1. Nickell S
    2. Förster F
    3. Linaroudis A
    4. Net WD
    5. Beck F
    6. Hegerl R
    7. Baumeister W
    8. Plitzko JM

    (2005) TOM software toolbox: acquisition and analysis for electron tomography

    Journal of Structural Biology 149:227–234.

    https://doi.org/10.1016/j.jsb.2004.10.006

    • PubMed
    • Google Scholar
34. 1. Noda T
    2. Sagara H
    3. Suzuki E
    4. Takada A
    5. Kida H
    6. Kawaoka Y

    (2002) Ebola virus VP40 drives the formation of virus-like filamentous particles along with GP

    Journal of Virology 76:4855–4865.

    https://doi.org/10.1128/JVI.76.10.4855-4865.2002

    • PubMed
    • Google Scholar
35. 1. Noda T
    2. Aoyama K
    3. Sagara H
    4. Kida H
    5. Kawaoka Y

    (2005) Nucleocapsid-like structures of ebola virus reconstructed using electron tomography

    Journal of Veterinary Medical Science 67:325–328.

    https://doi.org/10.1292/jvms.67.325

    • PubMed
    • Google Scholar
36. 1. Noda T
    2. Hagiwara K
    3. Sagara H
    4. Kawaoka Y

    (2010) Characterization of the ebola virus nucleoprotein-RNA complex

    Journal of General Virology 91:1478–1483.

    https://doi.org/10.1099/vir.0.019794-0

    • PubMed
    • Google Scholar
37. 1. Oda S
    2. Noda T
    3. Wijesinghe KJ
    4. Halfmann P
    5. Bornholdt ZA
    6. Abelson DM
    7. Armbrust T
    8. Stahelin RV
    9. Kawaoka Y
    10. Saphire EO

    (2016) Crystal structure of marburg virus VP40 reveals a broad, basic patch for matrix assembly and a requirement of the N-Terminal domain for immunosuppression

    Journal of Virology 90:1839–1848.

    https://doi.org/10.1128/JVI.01597-15

    • PubMed
    • Google Scholar
38. 1. Pettersen EF
    2. Goddard TD
    3. Huang CC
    4. Couch GS
    5. Greenblatt DM
    6. Meng EC
    7. Ferrin TE

    (2004) UCSF chimera--a visualization system for exploratory research and analysis

    Journal of Computational Chemistry 25:1605–1612.

    https://doi.org/10.1002/jcc.20084

    • PubMed
    • Google Scholar
39. 1. Pruggnaller S
    2. Mayr M
    3. Frangakis AS

    (2008) A visualization and segmentation toolbox for electron microscopy

    Journal of Structural Biology 164:161–165.

    https://doi.org/10.1016/j.jsb.2008.05.003

    • PubMed
    • Google Scholar
40. 1. Qu K
    2. Glass B
    3. Doležal M
    4. Schur FKM
    5. Murciano B
    6. Rein A
    7. Rumlová M
    8. Ruml T
    9. Kräusslich HG
    10. Briggs JAG

    (2018) Structure and architecture of immature and mature murine leukemia virus capsids

    PNAS 115:E11751–E11760.

    https://doi.org/10.1073/pnas.1811580115

    • PubMed
    • Google Scholar
41. 1. Rohou A
    2. Grigorieff N

    (2015) CTFFIND4: fast and accurate defocus estimation from electron micrographs

    Journal of Structural Biology 192:216–221.

    https://doi.org/10.1016/j.jsb.2015.08.008

    • PubMed
    • Google Scholar
42. 1. Schur FK
    2. Obr M
    3. Hagen WJ
    4. Wan W
    5. Jakobi AJ
    6. Kirkpatrick JM
    7. Sachse C
    8. Kräusslich HG
    9. Briggs JA

    (2016) An atomic model of HIV-1 capsid-SP1 reveals structures regulating assembly and maturation

    Science 353:506–508.

    https://doi.org/10.1126/science.aaf9620

    • PubMed
    • Google Scholar
43. 1. Timmins J
    2. Scianimanico S
    3. Schoehn G
    4. Weissenhorn W

    (2001) Vesicular release of ebola virus matrix protein VP40

    Virology 283:1–6.

    https://doi.org/10.1006/viro.2001.0860

    • PubMed
    • Google Scholar
44. 1. Vonrhein C
    2. Flensburg C
    3. Keller P
    4. Sharff A
    5. Smart O
    6. Paciorek W
    7. Womack T
    8. Bricogne G

    (2011) Data processing and analysis with the autoPROC toolbox

    Acta Crystallographica. Section D, Biological Crystallography 67:293–302.

    https://doi.org/10.1107/S0907444911007773

    • PubMed
    • Google Scholar
45. 1. Vonrhein C
    2. Tickle IJ
    3. Flensburg C
    4. Keller P
    5. Paciorek W
    6. Sharff A
    7. Bricogne G

    (2018) Advances in automated data analysis and processing within autoPROC , combined with improved characterisation, mitigation and visualisation of the anisotropy of diffraction limits using STARANISO

    Acta Crystallographica Section a Foundations and Advances 74:a360.

    https://doi.org/10.1107/S010876731809640X

    • Google Scholar
46. 1. Wan W
    2. Kolesnikova L
    3. Clarke M
    4. Koehler A
    5. Noda T
    6. Becker S
    7. Briggs JAG

    (2017) Structure and assembly of the ebola virus nucleocapsid

    Nature 551:394–397.

    https://doi.org/10.1038/nature24490

    • PubMed
    • Google Scholar
47. 1. Welsch S
    2. Kolesnikova L
    3. Krähling V
    4. Riches JD
    5. Becker S
    6. Briggs JA

    (2010) Electron tomography reveals the steps in Filovirus budding

    PLOS Pathogens 6:e1000875.

    https://doi.org/10.1371/journal.ppat.1000875

    • PubMed
    • Google Scholar
48. 1. Wenigenrath J
    2. Kolesnikova L
    3. Hoenen T
    4. Mittler E
    5. Becker S

    (2010) Establishment and application of an infectious virus-like particle system for marburg virus

    Journal of General Virology 91:1325–1334.

    https://doi.org/10.1099/vir.0.018226-0

    • PubMed
    • Google Scholar
49. 1. Xiong Q
    2. Morphew MK
    3. Schwartz CL
    4. Hoenger AH
    5. Mastronarde DN

    (2009) CTF determination and correction for low dose tomographic tilt series

    Journal of Structural Biology 168:378–387.

    https://doi.org/10.1016/j.jsb.2009.08.016

    • PubMed
    • Google Scholar

Author details

1. William Wan

   1. Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
   2. Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany

   Present address

   Department of Biochemistry and Center for Structural Biology Vanderbilt University, Nashville, United States

   Contribution

   Conceptualization, Formal analysis, Investigation, Visualization, Methodology, Writing - original draft, Writing - review and editing

   Competing interests

   No competing interests declared

   "This ORCID iD identifies the author of this article:" 0000-0003-2497-3010

2. Mairi Clarke

   Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany

   Contribution

   Investigation

   Competing interests

   No competing interests declared

   "This ORCID iD identifies the author of this article:" 0000-0002-9658-4308

3. Michael J Norris

   Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, United States

   Contribution

   Formal analysis, Investigation, Visualization, Writing - original draft, Writing - review and editing

   Competing interests

   No competing interests declared

   "This ORCID iD identifies the author of this article:" 0000-0002-8325-5257

4. Larissa Kolesnikova

   Institut für Virologie, Philipps-Universität Marburg, Hans-Meerwein-Straße, Marburg, Germany

   Contribution

   Resources, Writing - review and editing

   Competing interests

   No competing interests declared

5. Alexander Koehler

   Institut für Virologie, Philipps-Universität Marburg, Hans-Meerwein-Straße, Marburg, Germany

   Contribution

   Resources

   Competing interests

   No competing interests declared

6. Zachary A Bornholdt

   The Scripps Research Institute, La Jolla, United States

   Present address

   Mapp Biopharmaceutical, Inc, San Diego, United States

   Contribution

   Investigation

   Competing interests

   No competing interests declared

   "This ORCID iD identifies the author of this article:" 0000-0002-7557-9219

7. Stephan Becker

   Institut für Virologie, Philipps-Universität Marburg, Hans-Meerwein-Straße, Marburg, Germany

   Contribution

   Conceptualization, Supervision, Funding acquisition, Project administration, Writing - review and editing

   Competing interests

   No competing interests declared

8. Erica Ollmann Saphire

   Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, United States

   Contribution

   Conceptualization, Supervision, Funding acquisition, Writing - original draft, Project administration

   Competing interests

   No competing interests declared

   "This ORCID iD identifies the author of this article:" 0000-0002-1206-7451

9. John AG Briggs

   1. Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
   2. Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom

   Contribution

   Conceptualization, Supervision, Funding acquisition, Methodology, Writing - original draft, Project administration, Writing - review and editing

   For correspondence

   jbriggs@mrc-lmb.cam.ac.uk

   Competing interests

   No competing interests declared

   "This ORCID iD identifies the author of this article:" 0000-0003-3990-6910

• 2,907

  views

• 351

  downloads

• 48

  citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.