Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer and a glycosylated HIV-1 gp120 core
- University of Washington, United States
- Fred Hutchinson Cancer Research Center, United States
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, United States
Figures
Figure 1 with 6 supplements
Structural characterization of the 426c DS-SOSIP D3†-VRC01GL complex.
(A–B) BLI binding data of immobilized VRC01GL IgGs binding to WT 426c DS-SOSIP (A) or 426c DS-SOSIP D3 trimers. The concentrations of 426c DS-SOSIP trimers injected are indicated on each panel. Fit curves are colored as black dotted lines. A KD could not be determined in (A) due to the weak responses observed. The vertical dotted lines indicate the transition between association and dissociation phases. (C) Size-exclusion chromatogram of the purified 426c DS-SOSIP D3†-VRC01GL complex used for cryoEM structure determination. The pooled fractions used for cryoEM are highlighted in light blue. (D) Two orthogonal views of the 3.8 Å cryoEM reconstruction sharpened with a B-factor of −250 Å2 whereas the glycan density is shown unsharpened. (E) Two orthogonal views of the asymmetric 4.8 Å reconstruction with two bound Fabs. (F) Surface representation of the 426c SOSIP trimer highlighting differences in glycosylation compared to the BG505 SOSIP. Glycans not present in 426c are colored light-gray and outlined. Glycans present in the 426c strain but removed by mutation from the 426c DS-SOSIP D3† construct are colored magenta and outlined. The gp120 surface buried at the interface with VRC01GL is indicated as a dotted outline and is colored yellow. (G) Comparison of the gp120 bridging sheet conformation when VRC01GL-class Fabs are bound to either 426c DS-SOSIP D3† trimer (Top-left) or a previously solved 426c gp120 core lacking selected NLGSs, such as the Asn276 NLGS (PDB: 5IGX) (Top-right). Comparisons of β20β21 loop conformations of each complex are shown below corresponding top panels. (H) Comparison of glycan density and position between VRC01GL-bound and VRC01GL-free protomers in the asymmetric cryoEM reconstruction shown in (E). (Top) Asn197 and Asn386 glycan density is stronger for protomers bound to VRC01GL Fab than for the gp120 protomer not bound to VRC01GL (Bottom). In panels D-H, gp120 protomers are shown in blue, gp41 in red, N-linked glycans in green and VRC01GL in dark and light yellow for the heavy and light chains, respectively.
Figure 1—figure supplement 1
Multiple sequence alignment of analyzed HIV-1 426c constructs.
HIV-1 constructs derived from the 426c strain used in this study were subjected to multiple sequence alignment using Clustal Omega and rendered using ESPript (Gouet et al., 1999; Sievers and Higgins, 2014). Residues highlighted in red signify identical amino acids conserved across all aligned constructs. Similar residues are highlighted in bold and colored yellow.
Figure 1—figure supplement 2
Multiple sequence alignment of analyzed antibody and Fab constructs.
VRC01GL-class antibody and Fab constructs used in this study were subjected to multiple sequence alignment using Clustal Omega and rendered using ESPript (Gouet et al., 1999; Sievers and Higgins, 2014). Residues highlighted in red signify identical amino acids conserved across all aligned constructs. Similar residues are highlighted in bold and colored yellow.
Figure 1—figure supplement 3
Structural characterization of the 426c DS-SOSIP D3†-VRC01GL complex.
(A) Strategy implemented to increase the occupancy of VRC01GL Fab for structural studies. VRC01GL can engage 426c DS-SOSIP D3, but its low apparent affinity relative to VRC01GL IgG precludes saturation at the concentrations used for negative staining EM imaging (Left). Mild glutaraldehyde (GTA) crosslinking (0.25% GTA for 45 s followed by quenching with 1M Tris) increased VRC01GL saturation of 426c DS-SOSIP D3 (Middle). Engineering a disulfide bond between 426c DS-SOSIP D3 (G459Cgp120) and the heavy chain of VRC01GL (A60CHC) further increased gp120 saturation of the trimer (Right). (B) 3D reconstruction of negatively stained 426c DS-SOSIP D3†-VRC01GL. (C–D) Representative micrograph (E) and 2D class averages (F) of frozen-hydrated 426c DS-SOSIP D3†-VRC01GL. Scale bars represent 200 nm (E) or 200 Å (F). (E) Fourier shell correlation (FSC) curves of the 426c DS-SOSIP D3†-VRC01GL complex with three Fabs bound showing an estimated resolution of 3.8 Å. (F) Fourier shell correlation curves of the 426c DS-SOSIP D3†-VRC01GL complex with two Fabs bound showing an estimated resolution of 4.8 Å. The top and bottom horizontal dashed lines show the 0.5 and 0.143 cutoffs used for resolution estimates for map-to-model or gold-standard FSC, respectively. Both conventional FSC and FSC-part, as reported in Frealign, are shown.
Figure 1—figure supplement 4
Validation of the 426c DS-SOSIP D3†-VRC01GL cryoEM reconstructions.
(A) Local resolution estimates of 426c DS-SOSIP D3† bound to three copies of VRC01GL-A60CHC as determined using ResMap (Kucukelbir et al., 2014). (B) Graphical plot depicting distribution of particle image orientations. (C) Local resolution estimates of 426c DS-SOSIP D3† bound to two copies of VRC01GL-A60CHC as determined using ResMap(Kucukelbir et al., 2014). (D) Graphical plot depicting distribution of particle image orientations.
Figure 1—figure supplement 5
Comparison of gp120 interface contacts between VRC01GL and VRC01MAT.
Tables highlighting gp120 residues and their associated buried surface area (BSA) which comprise the interface with VRC01-class antibodies, as determined by PISA. BSA values are colored light gray for values ranging between 0.1 and 10.0, light blue for values between 10.1 and 30.0, dark blue for values between 30.1 and 50.0, and red for values > 50.0 Å2. HC: heavy chain; LC: light chain.
Figure 1—figure supplement 6
Example of glycans resolved in the 426c DS-SOSIP D3†-VRC01GL structure.
CryoEM density (green semi-transparent surface) and atomic model for glycans at positions Asn230, Asn197, Asn386 and Asn262 are shown.
Figure 2 with 1 supplement
Reintroduction of V5 loop NLGSs does not hinder VRC01GL binding to the 426c core.
(A–D) BLI curves and the corresponding equilibrium dissociation constants for VRC01GL IgG binding to the S278A/T462A/T465A (A), S278A/T462A (B), S278A/T465A (C), and S278A (D) 426c core constructs lacking either one or several glycans in the V5 and D loops. The concentrations of 426c core injected and the color key is indicated on each panel. Fitted curves are colored as black dotted lines. The vertical dashed lines indicate the transition between association and dissociation phases. (E) Ribbon diagram of the 426c core†-VRC01GL complex crystal structure. gp120 is colored blue, VRC01GL Fab is colored yellow (heavy chain: dark yellow; light chain: light yellow), and resolved gp120 glycans are shown in surface representation and colored green. (F) Close-up view of the gp120 Asn460 contacts with the backbone carbonyl and amide groups of the light chain VRC01GL residue Ile02. (G) Close-up view of the (GlcNAc)1 at position Asn463 of gp120. Oligosaccharides are labeled by the corresponding Asn residue they are linked to. Hydrogen bonds are represented as dashed lines. (H–I) Semi-quantitative LC-MS/MS analysis of VRC01GL-based IP experiments depicting the relative signal intensities for identified Asn460 (H) and Asn463 (I) glycoforms in unbound (blue), first binding event (red), and second binding event (yellow) fractions. The ‘unbound’ material indicates 426c core glycoforms that did not bind VRC01GL well following three binding steps. The ‘first’ binding event corresponds to 426c core elution fractions following collection of the sample flow-through and three rigorous wash cycles. The ‘second’ binding event follows a rebinding of the aforementioned flow-through, performing three additional washes, and eluting any residual bound material from the VRC01GL affinity column and collecting this fraction. Colored dots associated with their corresponding histogram bars represent individual values extracted from each experimental replicate, with the bar itself representing the experimental mean signal fraction.
Figure 2—figure supplement 1
Representative LC-MS/MS glycan identifications of 426c core constructs.
The top-left ribbon diagram corresponds to the sample analyzed. The LC-MS/MS fragmentation pattern is indicated in the top-right inset. A graphical depiction of the Asn276 residue (dotted white circle) and its associated identified glycan (blue: N-acetyl glucosamine, green: mannose) are represented on the spectrum. Green peak labels correspond to precursor peptides with/without LC-MS/MS fragmentation occurring within the glycan. Red/orange peak labels represent identified x, y, and z fragments. Blue/teal peak labels highlight identified a, b, and c fragments. A) Schematic of possible LC-MS/MS peptide fragmentation patterns. The peptide N- and C-termini are labeled. Possible fragmentation positions are denoted as grey text, with x, y, and z fragments represented as red/orange labels and blue/teal fragments representing a, b, and c fragments. Modified R-groups are denoted in red text. (B–C) Representative LC-MS/MS spectra of detected V5 glycosylation profile of the 426c core†-VRC01GL (GnTI-/--expressed) (B) and a ligand-free 426c core containing a glycan at position Asn460 (GnTI-/--expressed) (C). D–J) Various additional representative LC-MS/MS spectra of an Asn276 glycopeptide containing a (GlcNAc)2-(Man)5 oligosaccharide from ligand-free 426c core (HEK293F-expressed) (D), an Asn276 glycopeptide of the 426c core†-VRC01GL complex with a detectable (GlcNAc)2-(Man)4 sugar (GnTI-/--expressed) (E), an Asn276 peptide from the 426c core†-VRC01GL complex that is unglycosylated at position Asn276 (GnTI-/--expressed) (F), a 426c core Asn276 glycopeptide containing a (GlcNAc)2-(Man)5 oligosaccharide (GnTI-/--expressed) (G), a 426c S278T core Asn276 glycopeptide containing a (GlcNAc)2-(Man)5 oligosaccharide (GnTI-/--expressed) (H), and an Asn276 peptide of a 426c S278T core that is unglycosylated at position Asn276 (GnTI-/--expressed) (I).
Figure 3
The VRC01GL Fab bound to the 426c core in presence of a glycan at position Asn276.
(A–B) BLI binding data of the immobilized VRC01GL Fab with the 426c core expressed in either HEK293F (A) or HEK293 GnTI-/- cells (B). (C) Crystal structure of 426c core†-VRC01GL highlighting glycan electron density at position Asn276 (grey mesh: 2FO-Fc map contoured at 1.0σ) and amino-acid contacts for one molecule of the asymmetric unit. (D) Structure of VRC01MAT in complex (crosslinked) with the HIV-1 JR-FL SOSIP trimer (PDB ID: 5FYK) (Stewart-Jones et al., 2016) in the same orientation as in panel (C) and focusing on the glycan at position Asn276. (E) CryoEM structure of the 426c DS-SOSIP D3†-VRC01GL complex in the same orientation as in panel (C) and focusing on Asn276. Hydrogen bonds spanning 2.8–3.5 Å are depicted as dashed lines. (F–H) Comparison of VRC01GL CDRL1 conformations in the presence or absence of a glycan at position Asn276. In the three panels, gp120 is shown in blue cartoon representation and VRC01GL light chain in light yellow for our crystal structure of 426c core†-VRC01GL. Residues Gln27 to Tyr32 of VRC01GL light chain are shown as sticks and labeled. (F) VRC01GL bound to eODGT6 (PDB ID: 4JPK)(Jardine et al., 2013) is shown in grey. (G) Chain B of unliganded VRC01GL (PDB ID: 4JPI) (Jardine et al., 2013) is shown in cyan. (H) Chain L of unliganded VRC01GL (PDB ID: 4JPI) (Jardine et al., 2013) is shown in pink. (I) Semi-quantitative LC-MS/MS analysis depicting the relative signal intensities for identified Asn276 glycoforms in unbound (blue), after the first binding event (red), and after the second binding event (yellow) fractions taken from VRC01GL-based IP experiments. The ‘unbound’ material indicates 426c core glycoforms that did not bind VRC01GL following three binding events. Colored dots on corresponding histogram bars represent individual values extracted from each experimental replicate, with the bar itself representing the experimental mean signal fraction. (Inset) SDS-PAGE depicting the average molecular weight difference between wild-type 426c core species in ‘unbound’ flow-through and ‘bound’ elution fractions. (J) Structural comparison of VRC01GL CDRL1 conformations in the presence or absence of a glycan at position Asn276 in each of the molecules present in the asymmetric unit of our 426c core†-VRC01GL crystal structure.
Figure 4
VRC01GL binding in the presence of a glycan at position Asn276 and protection against EndoH-mediated digestion.
(A) Summary of identifications for 426c Asn276 glycopeptides. 426c core constructs that were subjected to qualitative LC-MS/MS are indicated on the left. Glycopeptide identifications detected using the Byonic software (Bern et al., 2012) are listed in blue and denoted with a check-mark (✓). (B–C) Representative LC-MS/MS spectra from panel (A) of glycan Asn276 identifications from the cross-linked 426c core†-VRC01GL and unliganded 426c core complex following EndoH digestion. The top-left ribbon diagram corresponds to the sample analyzed. The LC-MS/MS fragmentation pattern is indicated in the top-right inset. A graphical depiction of the Asn276 residue (dotted circle) and its associated identified glycan (blue: N-Acetylglucosamine, green : Mannose) are represented on the spectrum. The black line indicates identification of the precursor mass with neutral losses corresponding to the identified glycopeptide. Green peak labels correspond to precursor peptides with/without LC-MS/MS fragmentation occurring within the glycan. Red/orange peak labels represent identified x, y, and z fragments. Blue/teal peak labels highlight identified a, b, and c fragments. After EndoH digestion, a (GlcNAc)2-(Man)5 glycan was the predominant glycoform identified at position Asn276 with the sample used for crystallization (B) whereas a (GlcNAc)1 glycan prevailed with the unliganded 426c core (C).
Figure 5 with 2 supplements
Glycan length impacted VRC01GL IgG recognition of the 426c core.
(A) Semi-quantitative LC-MS/MS analysis depicting the relative signal intensities for identified Asn276 glycoforms in 426c core (blue), 426c S278T core (yellow), and 426c core expressed in the presence of 100 µM kifunensine (red). (Inset) SDS-PAGE demonstrating the molecular weight difference between the 426c core expressed in the absence (K-) or presence (K+) of 100 µM kifunensine. The molecular weights of the protein standards are indicated on the left. (B–E) BLI binding data and determined equilibrium dissociation constant values of VRC01GL IgG binding to the 426c core expressed using HEK293 GnTI-/- cells (B), the 426c core expressed using HEK293 GnTI-/- cells in the presence of 100 μM kifunensine (C), the 426c core expressed using HEK293 GnTI-/- cells and digested with EndoH (D), and the 426c S278A core expressed using HEK293 GnTI-/- cells (E). The concentrations of 426c core injected are indicated on each panel. Fitted curves are colored as black dotted lines. The vertical dotted lines indicate the transition between association and dissociation phases. N/D: not determined. (F–I) Semi-quantitative LC-MS/MS analysis depicting the relative signal intensities of unbound (blue), first binding event (red), and second binding event (yellow) fractions taken from VRC01GL-based IP experiments. Glycoforms were analyzed for NLGSs Asn197 (G), Asn289 (H), Asn337 (I), and Asn442 (J). Colored dots in panels A and F-I represent individual values extracted from each experimental replicate, with the bar itself representing the experimental mean signal fraction.
Figure 5—figure supplement 1
LC-MS/MS glycan identifications of kifunensine-treated 426c core constructs.
Representative LC-MS/MS spectra of glycan Asn276 identifications from the kifunensine-treated 426c core sample used for BLI experiments. The top-left ribbon diagram corresponds to the sample analyzed. The LC-MS/MS fragmentation pattern is indicated in the top-right inset. A graphical depiction of the Asn276 residue (dotted white circle) and its associated identified glycan (blue: N-acetyl glucosamine; green: mannose;) are represented on the spectrum. Green peak labels correspond to precursor peptides with/without LC-MS/MS fragmentation occurring within the glycan. Red/orange peak labels represent identified x, y, and z fragments. Blue/teal peak labels highlight identified a, b, and c fragments. (A–D) Representative LC-MS/MS spectra of an Asn276 glycopeptide with a (GlcNAc)2-(Man)5 oligosaccharide from the 426c core expressed in GnTI-/- cells in the presence of 100 µM kifunensine (A), an Asn276 glycopeptide with a (GlcNAc)2-(Man)8 oligosaccharide (B), an Asn276 glycopeptide with a (GlcNAc)2-(Man)9 oligosaccharide (C), and an unglycosylated Asn276 peptide (D). All these identifications were made from the same kifunensine-treated sample.
Figure 5—figure supplement 2
Trimeric 426c DS-SOSIP has a variable glycan length at position Asn276.
Representative LC-MS/MS spectra of glycan Asn276 identifications from the 426c DS-SOSIP. The top-left ribbon diagram corresponds to the sample analyzed. The LC-MS/MS fragmentation pattern is indicated in the top-right inset. A graphical depiction of the Asn276 residue (dotted white circle) and its associated identified glycan (green circle = Mannose; blue = N Acetylglucosamine) are represented on the spectrum. Green peak labels correspond to precursor peptides with/without LC-MS/MS fragmentation occurring within the glycan. Red/orange peak labels represent identified x, y, and z fragments. Blue/teal peak labels highlight identified a, b, and c fragments. (A–D) Representative LC-MS/MS spectrum of an Asn276 glyco-peptide of a detectable (GlcNAc)2-(Man)5 glycan (A), a (GlcNAc)2-(Man)6 glycan (B), a (GlcNAc)2-(Man)7 glycan (C), and a (GlcNAc)2-(Man)8 glycan (D).
Figure 6 with 1 supplement
Asn276 glycosylation frequency modulated VRC01GL-class IgGs recognition of the 426c core.
(A–D) BLI binding data and associated KD values of 426c core constructs, expressed in HEK293 GnTI-/- cells, with two immobilized VRC01GL-class IgGs. VRC01GL IgG binding was assessed against the 426c core (A) and the 426c S278T core (B). 12A21GL binding to the 426c core (C) and 426c S278T core (D) were also tested. (E–H) BLI binding data and corresponding KD values of 426c core constructs, expressed using HEK293 GnTI-/- cells and treated with EndoH, with VRC01GL-class IgGs. VRC01GL IgG binding was assessed against the EndoH-treated 426c core (E) and the 426c S278T core (F). 12A21GL interactions with the EndoH-treated 426c core (G) and 426c S278T core (H) were also tested. The concentrations of 426c core injected and the color key are indicated on each panel. Fit curves are colored as black dotted lines. The vertical dotted lines indicate the transition between association and dissociation phases.
Figure 6—figure supplement 1
VRC01GL binding affinity was not significantly affected by the identity of the residue 278 in the absence of a glycan at position Asn276.
(A) BLI kinetics parameters determined from panels (B–G) and Figure 6. (B–D) BLI binding data and determined equilibrium dissociation constants for VRC01GL IgG binding to 426c S278A core (A), 426c S278V core (B), and 426c S278R core. (E–G) BLI binding data and determined equilibrium dissociation constants of 12A21GL IgG binding to 426c S278A core (A), 426c S278V core (B), and 426c S278R core. The concentrations of 426c core injected are indicated on each panel. Fit curves are colored black. The vertical dashed lines indicate the transition between association and dissociation phases.
Tables
Table 1
CryoEM data collection, refinement, and model validation statistics.
https://doi.org/10.7554/eLife.37688.009| Parameter | Value |
|---|---|
| Data Collection | |
| No. of Micrographs | 1993 |
| No. of Particles | 134,443 |
| Pixel size, Å | 1.36 |
| Defocus range, μM | 2.0–3.5 |
| Voltage, kV | 300 |
| Dose Rate, counts/pix/sec | 8 |
| Electron dose, e-/Å2 | 43 |
| Refinement | |
| Resolution, Å | 3.8 |
| Map-sharpening B factor, Å2 | −230 |
| Model validation (3 Fab structure) | |
| Favored rotamers, % | 98.36% |
| Poor rotamers, % | 0.30% |
| Ramachandran outliers, % | 0.13% |
| Clash Score | 0.99 |
| Molprobity score EM ringer score | 1.02 1.97 |
Table 2
Crystallographic data collection and refinement statistics
https://doi.org/10.7554/eLife.37688.012| 426c core†-VRC01GL | |
|---|---|
| Data collection | |
| Space group | C2 |
| Cell dimensions | |
| a, b, c (Å) | 197.082, 109.003, 103.225 |
| α, β, γ (°) | 90.000, 114.468, 90.000 |
| Resolution (Å) | 50–2.32 (2.36–2.32)* |
| Rsym or Rmerge | 0.076 (0.643)* |
| I/sI | 23.4 (1.8)* |
| Completeness (%) | 95.6 (66.8)* |
| Redundancy | 7.4 (5.7)* |
| CC1/2 | (0.823)* |
| Refinement | |
| Resolution (Å) | 46.98–2.315 (2.398–2.315)* |
| No. reflections | 83086 |
| Rwork/Rfree | 24.38/29.55 (42.67/49.28) |
| No. atoms | 12470 |
| Protein | 11746 |
| Water | 325 |
| Ligand | 399 |
| B-factors (Å2) | 74.22 |
| Protein | 73.57 |
| Water | 69.62 |
| Ligand | 97.10 |
| R.m.s deviations | |
| Bond lengths (Å) | 0.003 |
| Bond angles (°) | 0.60 |
| Ramachadran Favored % | 93.39 |
| Ramachadran Outliers % | 0.13 |
| MolProbity all-atoms clashscore | 4.05 |
Key resources table
| Reagent type (species) or Resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Software, algorithm | Leginon | doi: 10.1016/ j.jsb.2005.03.010 | http://emg.nysbc.org/redmine/projects/leginon/wiki/Leginon_Homepage | |
| Software, algorithm | RELION-2 | doi: 10.1016/ j.jsb.2012.09.006 | RRID:SCR_016274 | http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page |
| Software, algorithm | MotionCor2 | doi:10.1038/ nmeth.4193 | http://emg.nysbc.org/redmine/projects/appion/wiki/Appion_Home | |
| Software, algorithm | GCTF | doi: 10.1016/ j.jsb.2015.11.003 | RRID:SCR_016500 | https://www.mrc-lmb.cam.ac.uk/kzhang/ |
| Software, algorithm | CTFFIND4 | doi:10.1016/ j.jsb.2015.08.008 | http://grigoriefflab.janelia.org/ctffind4 | |
| Software, algorithm | Frealign | doi: 10.1016/ bs.mie.2016.04.013 | http://grigoriefflab.janelia.org/frealign | |
| Software, algorithm | Appion Package | doi: 10.1016/ j.jsb.2009.01.002 | http://emg.nysbc.org/redmine/projects/appion/wiki/Appion_Home | |
| Software, algorithm | DoG Picker | doi:10.1016/ j.jsb.2009.01.004 | http://emg.nysbc.org/redmine/projects/appion/wiki/Appion_Home | |
| Software, algorithm | Coot | doi: 10.1107/ S0907444910007493 | RRID:SCR_014222 | http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/devel/build-info.html |
| Software, algorithm | Rosetta | doi: 10.1146/annurev. biochem.77.062906 .171838 | RRID:SCR_015701 | https://www.rosettacommons.org/software |
| Software, algorithm | UCSF Chimera | doi: 10.1002/jcc.20084 | RRID:SCR_004097 | http://plato.cgl.ucsf.edu/chimera/ |
| Software, algorithm | PMI-Byonic | doi: 10.1002/ 0471250953.bi1320s40 | https://www.proteinmetrics.com/products/byonic/ | |
| Software, algorithm | Skyline | doi: 10.1093/ bioinformatics/btq054 | RRID:SCR_014080 | https://skyline.ms/project/home/software/Skyline/begin.view |
| Software, algorithm | Octet Data Acquisition | Pall ForteBio | CFR 10.0.3.12d | https://www.fortebio.com/octet-software.html |
| Software, algorithm | Octet Data Analysis | Pall ForteBio | CFR 10.0.3.1 | https://www.fortebio.com/octet-software.html |
| Software, algorithm | Phaser | doi:10.1107/ S0021889807021206 | https://www.phenix-online.org/documentation/reference/phaser.html | |
| Software, algorithm | Phenix.refine | doi:10.1107/ S0907444912001308 | https://www.phenix-online.org/documentation/reference/refinement.html | |
| Software, algorithm | GraphPad Prism | GraphPad | RRID:SCR_002798 | https://www.graphpad.com/scientific-software/prism/ |
| Software, algorithm | Pymol | Delano, 2002 | https://pymol.org/2/ | |
| Cell Line (Homo sapiens) | HEK293S GnTI-/- | ATCC | ATCC: CRL-3022; RRID:CVCL_A785 | https://www.atcc.org/Products/All/CRL-3022.aspx |
| Cell Line (Homo sapiens) | HEK293F | ThermoFisher Scientifc | Cat# R79007 | https://www.thermofisher.com/order/catalog/product/R79007 |
| Gene (Homo sapiens) | gl VRC01 Igk(3-11) | doi: 10.1126/ science.1192819 | ||
| Gene (Homo sapiens) | gl VRC01 Igg Fab | doi: 10.1038/ ncomms10618 | ||
| Gene (Homo sapiens) | gl VRC01 Igg Fab A60C/C98S | This paper | ||
| Gene (Homo sapiens) | gl VRC01 Igg | 10.1126/science.1192819 | ||
| Gene (Homo sapiens) | gl 12A21 Igk(1-33) | 10.1084/jem.20122824 | ||
| Gene (Homo sapiens) | gl 12A21 Igg Fab | 10.1038/ncomms10618 | ||
| Gene (Homo sapiens) | gl 12A21 Igg | 10.1084/jem.20122824 | ||
| Strain, strain background (Human Immunodeficiency Virus-1, Strain: 426 c) | WT_426 c_DS-SOSIP | 10.1016/j.cell .2016.07.029 | ||
| Strain, strain background (Human Immunodeficiency Virus-1, Strain: 426 c) | 426 c_G459C _DS-SOSIP_D3 | This paper | ||
| Strain, strain background (Human Immunodeficiency Virus-1, Strain: 426 c) | 426 c_WT_ gp120c_core | This paper | ||
| Strain, strain background (Human Immunodeficiency Virus-1, Strain: 426 c) | 426 c_G459C _gp120c_core | This paper | ||
| Strain, strain background (Human Immunodeficiency Virus-1, Strain: 426 c) | 426 c_S278A _gp120c_core | This paper | ||
| Strain, strain background (Human Immunodeficiency Virus-1, Strain: 426 c) | 426 c_S278A_T462A _gp120c_core | This paper | ||
| Strain, strain background (Human Immunodeficiency Virus-1, Strain: 426 c) | 426 c_S278A_T465A _gp120c_core | This paper | ||
| Strain, strain background (Human Immunodeficiency Virus-1, Strain: 426 c) | 426 c_S278A_T462A_ T465A_gp120c_core | This paper | ||
| Strain, strain background (Human Immunodeficiency Virus-1, Strain: 426 c) | 426 c_S278T_gp120c | This paper | ||
| Recombinant DNA reagent | pTT3 | PMID: 11788735 | https://biochimie.umontreal.ca/en/department/professors/yves-durocher/ | |
| Recombinant DNA reagent | pVRC8400 | NIH | ||
| Chemical compound, drug | Kifunensine | Sigma-Aldrich | CAS Number 109944-15-2 | https://www.sigmaaldrich.com/catalog/product/sigma/k1140?lang=en®ion=US&gclid=Cj0KCQjwr53OBRCDARIsAL0vKrNtYwTyRzHU65HyVBwdntcP3kGpZ0ElVwYeSK3OcorLn0wf8U1iMQgaAssSEALw_wcB |
| Peptide, recombinant protein | Endoglycosidase-H | New England Biolabs | Catalog #P0702S | https://www.neb.com/products/p0702-endo-h#Product%20Information |
Additional files
-
Supplementary file 1
BLI kinetics parameters of various 426c core constructs expressed using HEK293F cells.
- https://doi.org/10.7554/eLife.37688.020
-
Supplementary file 2
RMSD Table comparing unliganded and liganded VRC01GL CDRL1 loop conformations.
- https://doi.org/10.7554/eLife.37688.021
-
Supplementary file 3
BLI kinetics parameters of various 426c core constructs expressed using GnTI-/- cells.
- https://doi.org/10.7554/eLife.37688.022
-
Transparent reporting form
- https://doi.org/10.7554/eLife.37688.023
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Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer and a glycosylated HIV-1 gp120 core
eLife 7:e37688.
https://doi.org/10.7554/eLife.37688
