Structural basis of Plasmodium vivax inhibition by antibodies binding to the circumsporozoite protein repeats

  1. Iga Kucharska
  2. Lamia Hossain
  3. Danton Ivanochko
  4. Qiren Yang
  5. John L Rubinstein
  6. Régis Pomès
  7. Jean-Philippe Julien  Is a corresponding author
  1. Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Canada
  2. Department of Biochemistry, University of Toronto, Canada
  3. Department of Medical Biophysics, University of Toronto, Canada
  4. Department of Immunology, University of Toronto, Canada
7 figures, 2 tables and 3 additional files

Figures

Comparison of PvCSPvk210 and PvCSPvk247 repeat sequences.

(A) Schematic representations of PvCSPvk210 and PvCSPvk247 sequences, each including an N-terminal domain, central repeat region, and C-terminal domain. Colored blocks represent repeat motifs. The sequence of peptides used in circular dichroism (CD) spectroscopy studies is shown below. (B) Superimposition of the CD spectra obtained for PvCSPvk210 (top panel) and PvCSP247 peptides (bottom panel). PvCSPvk210 peptides 210-1, 210-2, 210-3, 210-4, and 210-5 are colored from navy to light blue; PvCSPvk247 peptides are depicted in green (247-1), yellow (247-2), and orange (247-3), respectively.

Figure 2 with 2 supplements
Conformational flexibility of PvCSPvk210 and PvCSPvk247 peptides.

(A) Superposition of the conformations of peptides resulting from molecular dynamics (MD) simulations at every 2 ns and aligned to the conformational median structure. (B) Example snapshots of the highest (peptides 210-7, 210-8, 210-9, and 247-3) or the second highest (peptides 210-6, 247-1, 247-2) propensity β-turn for each peptide. Color coding of atoms: oxygen (red), nitrogen (blue), and hydrogen (white). For clarity, only the hydrogen atom involved in the H-bonded turn is shown. H-bond between C=O of residue i and N–H of residue i + 3 is shown as a gray line. (C) Secondary structure propensity at each residue, averaged over 20 replicas and computed using the Dictionary of Secondary Structure for Proteins (DSSP) criteria (Nagy and Oostenbrink, 2014). (D) Elastic modulus of peptides computed from MD simulations. The reversible work or free energy (ΔG) for extension and compression of the peptide is plotted as a function of equilibrium end-to-end distances (dEE) (solid line). The data is fitted to the quadratic function of elastic potential energy (black dashed line). For each peptide, the estimated values of k (elastic modulus), d0 (equilibrium dEE), and R2 (regression coefficient to indicate quality of fit) are shown. Shading represents standard error of mean.

Figure 2—figure supplement 1
Time evolution of structural properties of PvCSP peptides.

Properties are averaged over 20 replicas, with the shading area representing standard error of the mean. (A) H-bond turn propensity (Xturn). (B) Number of peptide-peptide H-bonds per residue (XHB).

Figure 2—figure supplement 2
Ensemble-averaged backbone-backbone H-bonding maps for each PvCSP peptide sequence.

A forward H-bond forms between C=O (acceptor) of residue i and N–H (donor) of residue i + n (upper diagonal), while the reverse forms a reverse H-bond (lower diagonal). Within the diagonal represents local interactions, which forms by a pair of residues that are less than seven residues apart. The color of each square represents the H-bond propensities formed by the interacting residues. The gray and the pink arrows indicate the highest and the second highest propensity turn, respectively.

Figure 3 with 4 supplements
2F2 Fab binding to PvCSPvk210 repeat peptides.

(A) Affinities of 2F2 Fab for peptides 210-1, 210-2, 210-3, 210-4, and 210-5 as measured by isothermal titration calorimetry (ITC). Open circles represent independent measurements. Mean binding constant (KD) and binding stoichiometry (N) values are shown above the corresponding bar. Error bars represent SEM. (B) Upper panel: sequences of peptides used in ITC experiments with variable residues underlined. Dark gray denotes the core epitope of the peptide resolved in all the X-ray crystal structures, and light gray shading indicates residues resolved in the corresponding X-ray crystal structures. Bottom panel: comparison of the conformations of PvCSP210 peptides in X-ray crystal structures. PvCSPvk210 peptides are colored from navy to light blue, with the residues adopting one turn of a 310-helix depicted in pink. (C) Top and side views of the 210-4 peptide (light blue) in the binding groove of the 2F2 Fab shown as surface representation (heavy chain [HC] shown in green and kappa chain [KC] shown in white). (D) Comparison of the conformations adopted by the core epitope of peptides 210-1, 210-2, 210-3, 210-4, and 210-5 when bound to 2F2. (E) Detailed interactions between Fab 2F2 and peptide 210-4. H-bonds and salt bridges are shown as black dashes, peptide 210-4 is shown in light blue, HC is shown in green, and KC is shown in gray. Fab residues are annotated with H or K letters to indicate heavy and kappa light chain, respectively.

Figure 3—figure supplement 1
Isothermal titration calorimetry (ITC) measurements of 2F2 Fab binding to peptides 210-1 (A), 210-2 (B), 210-3 (C), 210-4 (D), and 210-5 (E).
Figure 3—figure supplement 2
Stereo-image of the composite omit map electron density contoured at 1.0–1.2 sigma for peptides 210-1 (A), 210-2 (B), 210-3 (C), 210-4 (D), and 210-5 (E).
Figure 3—figure supplement 3
Interactions between germline-encoded aromatic residues in anti-CSP monoclonal antibodies (mAbs) and repeat peptides.

Heavy chain complementarity-determining region (HCDR) and kappa chain complementarity-determining region (KCDR) are colored green and gray, respectively. The positions of germline-encoded tryptophan and tyrosine residues interacting with the peptides are highlighted with black dashed circles. (A) 1210 Fab (Imkeller et al., 2018) and NANP5 peptide (pink); (B, D) 2E10.E9 Fab and 247-4 peptide (orange); (C, E) 2F2 Fab and 210-3 peptide (blue). (F) Interactions between peptide proline residues and H.Trp52 in 1210 Fab (left panel) and H.Trp50 in 2E10.E9 Fab (right panel). (G) Residues 8PAG10 of PvCSPvk210 peptides adopt one turn of a 310-helix, which is positioned in the pocket formed by aromatic residues of KCDR1 and 3.

Figure 3—figure supplement 4
Electrostatic surface potential of monoclonal antibodies (mAbs) 2F2 (A), 2E10.E9 (B), 1210 (Imkeller et al., 2018) (C), and 3D11 (Kucharska et al., 2020) (D) bound to CSP peptides.

Scale: –5 kT e–1 (red) to +5 kT e–1 (blue).

Figure 4 with 2 supplements
2E10.E9 Fab binding to PvCSPvk247 repeat peptides.

(A) Affinities of 2E10.E9 Fab for peptides 247-1, 247-2, 247-3, and 247-4 as measured by isothermal titration calorimetry (ITC). Open circles represent independent measurements. Mean binding constant (KD) and binding stoichiometry (N) values are shown above the corresponding bar. Error bars represent SEM. (B) Upper panel: sequences of peptides used in ITC with variable residues underlined. Dark gray denotes the core epitope of the peptide resolved in all X-ray crystal structures, and light gray shading indicates residues resolved in the corresponding X-ray crystal structures. Bottom panel: comparison of the conformations of PvCSP247 peptides in X-ray crystal structures, with peptides 247-2, 247-3, and 247-4 depicted in yellow, orange, and teal, respectively. (C) Top and side views of the 247-3 peptide (orange) in the binding groove of the 2E10.E9 Fab shown as surface representation (heavy chain [HC] shown in blue and kappa chain [KC] shown in white). (D) Comparison of the conformations adopted by the core epitope of peptides 247-2, 247-3, and 247-4 when bound to 2E10.E9. (E) Detailed interactions between Fab 2E10.E9 and peptide 247-3. H-bonds are shown as black dashes, peptide 247-3 is shown in orange, HC is shown in green, and KC is shown in gray. The Fab residues are annotated with H or K letters to indicate heavy and kappa light chain, respectively.

Figure 4—figure supplement 1
Isothermal titration calorimetry (ITC) measurements of 2E10.E9 Fab binding to peptides 247-1 (A), 247-2 (B), 24-3 (C), and 247-4 (D).
Figure 4—figure supplement 2
Stereo-image of the composite omit map electron density contoured at 1.2 sigma for peptides 247-2 (A), 247-3 (B), and 247-4 (C).
Homotypic Fab-Fab interactions in Fab 2E10.E9-247-2 peptide complex.

(A, B) 2E10.E9 Fabs that simultaneously recognize the 247-2 peptide contact each other through an interface consisting of mainly of heavy chain complementarity-determining region (HCDR)2 of both Fab A and B, as well as kappa chain complementarity-determining region (KCDR)3 of Fab A. The heavy chain (HC) of Fab A and B is colored light and dark blue, respectively. The kappa chain (KC) of Fab A and B is colored light and dark gray, respectively. HCDR1, 2, and 3 are colored light pink, dark pink, and purple, respectively. KCDR1, 2, and 3 are shown in light brown, dark brown, and red, respectively. The 247-2 peptide is depicted in yellow. Black dashed lines denote H-bonds. Residues forming Fab-Fab contacts are labeled with the position of the Fab (A or B) indicated in subscript. (C) Sequence alignment of monoclonal antibody (mAb) 2E10.E9 with its inferred germline precursor. Yellow highlight: residues involved in homotypic interactions; green highlight: residues involved in homotypic interactions that form H-bonds.

Figure 6 with 1 supplement
Binding of 2F2 and 2E10.E9 to full-length PvCSPvk210 and PvCSPvk247.

Binding kinetics of twofold dilutions of 2F2 IgG and Fab (A, upper panel and lower panel, respectively) to PvCSPvk210, and 2E10.E9 IgG and Fab (B, upper panel and lower panel, respectively) to PvCSPvk247, as measured by biolayer interferometry (BLI). Representative sensograms are shown in black and 2:1 model best fits in red. Data shown are representative of three independent measurements. Isothermal titration calorimetry (ITC) analysis of 2F2 Fab binding to PvCSPvk210 (C) and 2E10.E9 Fab binding to PvCSPvk247 (D) at 25°C. (C, top panels): raw data of PvCSPvk210 (5 µM) in the sample cell titrated with 2F2 Fab (240 µM) in the syringe. (D, top panels): raw data of PvCSPvk247 (5 µM) in the sample cell titrated with 2E10.E9 Fab (400 µM) in the syringe. (C, D, bottom panel): plot and trendline of heat of injectant corresponding to the raw data. Results from size-exclusion chromatography coupled with multiangle light scattering (SEC-MALS) for the Fab 2F2-PvCSPvk210 sample (E, left panel) and 2E10.E9 Fab-PvCSPvk247 (F, left panel) sample, where the Fabs are in molar excess. Measurement of the molar mass of the eluting complex is shown as a red line. Mean molar mass is indicated. SDS-PAGE analysis of resulting peaks 1 and 2 for 2F2 Fab-PvCSPvk210 (E, right panel) and 2E10.E9 Fab-PvCSPvk247 (F, right panel) samples from SEC-MALS. Each peak was sampled in reducing and nonreducing conditions as indicated by + and –, respectively.

Figure 6—source data 1

SDS-PAGE analysis of 2F2 Fab-PvCSPvk210 and 2E10.E9 Fab-PvCSPvk247 complexes.

https://cdn.elifesciences.org/articles/72908/elife-72908-fig6-data1-v2.zip
Figure 6—figure supplement 1
Negative stain electron microscopy (NS EM) and electron cryomicroscopy (cryo-EM) analysis of 2E10.E9 Fab-PvCSPvk247 (A) and 2F2 Fab-PvCSPvk210 (B) complexes.

Upper panels show representative NS EM (left panel) and cryo-EM (right panel) micrographs. Positions of representative individual particles are highlighted with white circles. Lower panels: representative NS EM (left panel) and cryo-EM (right panel) 2D class averages. Scale bars on micrographs: 100 nm. Scale bars on 2D classes: 10 nm.

Evaluation of flexibility for various Fab-CSP peptide complexes by negative stain electron microscopy.

Refined 3D classes (upper panels) and representative 2D class averages (bottom panels) of (A) 2F2 Fab-210-10 peptide, (B) 2E10.E9 Fab-247-2 peptide, (C) 3D11 Fab-NPNDx2 peptide (PPPPNPND)3 (Kucharska et al., 2020), and (D) 1210 Fab-(NANP)5 peptide (Imkeller et al., 2018) complexes. The approximate angle between adjacent Fabs in each class is indicated. Scale bars on 3D and 2D classes: 50 nm.

Tables

Table 1
X-ray crystallography data collection and refinement statistics.
2F2-210-12F2-210-22F2-210-32F2-210-42F2-210-52E10-247-22E10-247-32E10-247-4
BeamlineAPS 23-ID-BAPS 23-ID-DAPS 23-ID-BAPS 23-ID-BAPS 23-ID-DAPS 23-ID-BAPS 23-ID-BAPS 23-ID-D
Wavelength (Å)1.0331671.0331671.0331671.0331671.0331671.0331671.0331671.033200
Space groupP 1C 2C 2P 1C 2P 31P 21P 1
Cell dimensions71.5, 81.4, 82.392.9, 60.4, 158.392.6, 60.8, 81.471.7, 82.3, 82.893.4, 60.5, 159.1142.4, 142.4, 91.356.4, 144.4, 60.554.5, 66.3, 142.3
α, β, γ (o)94.6, 114.1, 111.690, 101.5, 9090, 101.6, 9095.3, 113.8, 111.590, 101.2, 9090, 90, 12090, 102.8, 90100.4, 92.3, 91.7
Resolution (Å)*29.48–2.20 (2.25–2.20)29.21–2.54 (2.65–2.54)29.71–1.97(2.02–1.97)29.61–2.67 (2.77–2.67)29.69–2.27 (2.34–2.27)29.55–3.19 (3.30–3.19)29.48–2.68 (2.78–2.68)29.34–2.71 (2.81–2.71)
No. molecules in the asymmetric unit (ASU)32132224
No. observations264,344 (16,542)181,285 (21,112)101,891 (4384)155,413 (16,123)471,275 (38,772)693,999 (70,530)184,740 (18,748)552,431 (55,667)
No. unique observations75,088 (4440)28,642 (3484)31,038 (1962)43,179 (4542)40,512 (3722)34,411 (3469)26,439 (2627)53,126 (5316)
Multiplicity3.5 (3.7)6.3 (6.1)3.3 (2.2)4.7 (1.5)11.6 (10.3)20.1 (20.3)7.0 (7.1)10.4 (10.5)
Rmerge (%)15.5 (95.2)16.4 (144.5)6.5 (55.7)13.9 (62.8)34.2 (175.0)36.1 (370.6)21.6 (158.6)22.4 (123.5)
Rpim (%) 7.5 (32.4)10.6 (97.6)6.1 (46.9)7.8 (30.8)15.3 (83.0)8.2 (84.0)8.8 (63.7)7.3 (39.8)
< I/σ I>5.2 (1.5)6.7 (1.5)8.3 (1.5)4.7 (1.5)9.4 (1.5)13.2 (1.7)9.2 (1.6)7.4 (1.6)
CC1/20.965 (0.527)0.994 (0.529)0.996 (0.603)0.987 (0.669)0.927 (0.435)0.998 (0.756)0.993 (0.578)0.995 (0.729)
Completeness (%)97.5 (97.1)99.8 (100.0)98.7 (90.5)98.3 (97.8)99.9 (100.0)99.8 (99.6)99.9 (100.0)100.0 (100.0)
Refinement statistics
Reflections used in refinement74,67228,60431,03043,16040,50134,41126,43953,126
Reflections used for R-free37311432155221622026173213142067
Non-hydrogen atoms10,5806872359510,50469416818688513,707
Macromolecule10,1236864341810,34468416818684513,620
Water4338177160100-3487
Heteroatom------6-
R §work/Rfree17.9/22.020.2/24.918.6/23.518.6/22.819.2/23.818.0/21.020.7/23.920.9/24.6
Rms deviations from ideality
Bond lengths (Å)0.0070.0020.0150.0020.0030.0100.0100.010
Bond angle (°)0.870.511.330.570.711.391.251.22
Ramachandran plot
Favored regions (%)97.597.997.397.998.694.697.197.5
Allowed regions (%)2.32.12.71.91.45.42.92.5
B-factors (A2)
Wilson B-value39.164.735.547.050.091.042.154.7
Average B-factors45.775.045.751.053.7111.071.077.0
Average macromolecule45.775.945.951.153.7111.071.477.2
Average heteroatom------69.8-
Average water molecule44.061.441.141.954.3-37.843.3
  1. *

    Values in parentheses refer to the highest resolution bin.

  2. Rmerge = ∑hkl ∑i | Ihkl, i -< Ihkl > | / ∑hkl< Ihkl > .

  3. Rpim = ∑hkl [1/(N – 1)]1/2 ∑i | Ihkl, i -< Ihkl > | / ∑hkl< Ihkl > .

  4. §

    Rwork = (∑ | |Fo | - |Fc | |) / (∑ | |Fo |).

  5. 5% of data were used for the Rfree calculation.

Key resources table
Reagent type (species) or resourceDesignationSource or referenceIdentifiersAdditional information
Recombinant DNA reagentpcDNA3.4-2F2
Fab HC (plasmid)
This paperN/A2F2 Fab heavy chain gene in pcDNA3.4 TOPO vector
Recombinant DNA reagentpcDNA3.4-2F2
KC (plasmid)
This paperN/A2F2 light chain gene in pcDNA3.4 TOPO vector
Recombinant DNA reagentpcDNA3.4-2E10.E9
Fab HC (plasmid)
This paperN/A2E10.E9 Fab heavy chain gene in pcDNA3.4 TOPO vector
Recombinant DNA reagentpcDNA3.4-2E10.E9
KC (plasmid)
This paperN/A2E10.E9 light chain gene in pcDNA3.4 TOPO vector
Recombinant DNA reagentpcDNA3.4-
PvCSPvk210-
His6x (plasmid)
This paperN/APvCSPvk210 gene with His tag in pcDNA3.4 TOPO vector
Recombinant DNA reagentpcDNA3.4-
PvCSPvk247-
His6x (plasmid)
This paperN/APvCSPvk247 gene with His tag in pcDNA3.4 TOPO vector
Cell line (Homo sapiens)FreeStyle
293F cells
Thermo Fisher ScientificCat# R79007
Cell line (Mus musculus)2F2
hybridoma cell line
Nardin et al., 1982, Alan Cochrane, unpublished resultsBEI Resources #MRA-184; RRID:CVCL_A7VR
Cell line (M. musculus)2E10.E9
hybridoma cell line
Nardin et al., 1982, Alan Cochrane, unpublished resultsBEI Resources #MRA-185; RRID:CVCL_A7VT
Chemical compound, drugGibco FreeStyle
293 Expression
Medium
Thermo Fisher ScientificCat# 12338026
Chemical compound, drugGibco
Hybridoma-SFM
Thermo Fisher ScientificCat# 12045076
Chemical compound, drugFectoPRO DNA
Transfection
Reagent
VWRCat# 10118-444
Chemical compound, drugFetal bovine
serum
Thermo Fisher ScientificCat# 12483-020
Antibody2F2 IgG
(mouse
monoclonal)
Nardin et al., 1982, Alan Cochrane, unpublished resultsN/APurified from 2F2 hybridoma cell line; see Materials and methods
Antibody2E10.E9 IgG
(mouse
monoclonal)
Nardin et al., 1982, Alan Cochrane, unpublished resultsN/APurified from 2E10.E9 hybridoma cell line; see Materials and methods
Biological sample (Carica papaya)Papain from
papaya latex
Sigma-AldrichCat# P4762
Peptide, recombinant protein1210 FabImkeller et al., 2018N/ASee Materials and methods for concentrations and masses used, and buffer conditions
Peptide, recombinant protein3D11 FabKucharska et al., 2020N/ASee Materials and methods for concentrations and masses used, and buffer conditions
Peptide, recombinant protein2F2 FabThis paperN/ASee Materials and methods for concentrations and masses used, and buffer conditions
Peptide, recombinant protein2E10.E9 FabThis paperN/ASee Materials and methods for concentrations and masses used, and buffer conditions
Peptide, recombinant protein210-1
(GDRADGQ
PAGDRADGQPA)
This paperN/ADerived from PvCSPvk210 repeat region
Peptide, recombinant protein210-2
(GDRAAGQ
PAGDRAAGQPA)
This paperN/ADerived from PvCSPvk210 repeat region
Peptide, recombinant protein210-3
(GDRADGQP
AGDRAAGQPA)
This paperN/ADerived from PvCSPvk210 repeat region
Peptide, recombinant protein210-4
(GDRAAGQ
PAGDRADGQP)
This paperN/ADerived from PvCSPvk210 repeat region
Peptide, recombinant protein210-5
(GDRAAGQ
PAGNGAGGQAA)
This paperN/ADerived from PvCSPvk210 repeat region
Peptide, recombinant protein210-6
(GDRADGQ
PAGDRADGQ
PAGDRADGQPA)
This paperN/ADerived from PvCSPvk210 repeat region
Peptide, recombinant protein210-7
(GDRAAGQ
PAGDRAAGQ
PAGDRAAGQPA)
This paperN/ADerived from PvCSPvk210 repeat region
Peptide, recombinant protein210-8
(GDRADGQ
PAGDRAAGQ
PAGDRADGQPA)
This paperN/ADerived from PvCSPvk210 repeat region
Peptide, recombinant protein210-9
(GDRAAGQ
PAGDRAAGQ
PAGNGAGGQAA)
This paperN/ADerived from PvCSPvk210 repeat region
Peptide, recombinant protein210-10
(GDRADGQ
PAGDRADGQ
PAGDRADGQ
PAGDRADGQPA)
This paperN/ADerived from PvCSPvk210 repeat region
Peptide, recombinant protein247-1
(ANGAGNQ
PGANGAGNQ
PGANGAGNQPG)
This paperN/ADerived from PvCSPvk247 repeat region
Peptide, recombinant protein247-2
(EDGAGNQ
PGANGAGNQ
PGANGAGNQPG)
This paperN/ADerived from PvCSPvk247 repeat region
Peptide, recombinant protein247-3
(ANGAGNQ
PGANGAGNQ
PGANGAGGQAA)
This paperN/ADerived from PvCSPvk247 repeat region
Peptide, recombinant protein247-4
(ANGAGNQ
PGANGAGNQPG)
This paperN/ADerived from PvCSPvk247 repeat region
Peptide, recombinant proteinNPNDx2
(PPPPNPNDP
PPPNPNDP
PPPNPND)
Kucharska et al., 2020N/ADerived from PbCSP ANKA repeat region
Peptide, recombinant proteinNANP5
(NANPNAN
PNANPNA
NPNANP)
Imkeller et al., 2018N/ADerived from PfCSP NF54 repeat region
Software, algorithmGROMACS 2016.5Abraham et al., 2015; Berendsen et al., 1995https://manual.gromacs.org/documentation/2016-current/index.html;RRID:SCR_014565
Software, algorithmCHARMM22*Best and Hummer, 2009; Best and Mittal, 2010; Lindorff-Larsen et al., 2012; MacKerell et al., 1998; Piana et al., 2011https://www.charmm.org/charmm/?CFID=66837e22-4ee5-47ba-bcbf-b4b385c2397e&CFTOKEN=0; RRID:SCR_014892
Software, algorithmLINCSHess, 2008N/A
Software, algorithmParticle-Mesh
Ewald algorithm
Darden et al., 1993; Essmann et al., 1995N/A
Software, algorithmParrinello–Rahman algorithmParrinello and Rahman, 1981N/A
Software, algorithmVMDHumphrey et al., 1996https://www.ks.uiuc.edu/Research/vmd/; RRID:SCR_001820
Software, algorithmMatplotlibHunter, 2007https://matplotlib.org/; RRID:SCR_008624
Software, algorithmMDTrajMcGibbon et al., 2015https://www.mdtraj.org/1.9.5/index.html
Software, algorithmOctet Data AnalysisSoftware 9.0.0.6ForteBiohttps://www.fortebio.com/products/octet-systems-software
Software, algorithmMicroCal ITC Origin7.0 Analysis SoftwareMalvernhttps://www.malvernpanalytical.com/
Software, algorithmASTRAWyatthttps://www.wyatt.com/products/software/astra.html; RRID:SCR_016255
Software, algorithmGraphPad Prism 8GraphPad Softwarehttps://www.graphpad.com/; RRID:SCR_002798
Software, algorithmSBGridSBGrid Consortiumhttps://sbgrid.org/; RRID:SCR_003511
Software, algorithmcryoSPARC v2Punjani et al., 2017https://cryosparc.com/; RRID:SCR_016501
Software, algorithmRelionScheres, 2012https://www3.mrc-lmb.cam.ac.uk/relion/; RRID:SCR_016274
Software, algorithmXDSKabsch, 2010http://xds.mpimf-heidelberg.mpg.de/; RRID:SCR_015652
Software, algorithmPhaserMcCoy et al., 2007https://www.phenix-online.org/; RRID:SCR_014224
Software, algorithmPhenix (phenix.
refine; phenix.real_
space_refine)
Adams et al., 2010https://www.phenix-online.org/; RRID:SCR_014224
Software, algorithmUCSF ChimeraPettersen et al., 2004https://www.cgl.ucsf.edu/chimera/; RRID:SCR_004097
Software, algorithmUCSF ChimeraXGoddard et al., 2018https://www.cgl.ucsf.edu/chimerax/; RRID:SCR_015872
Software, algorithmCootEmsley et al., 2010https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/; RRID:SCR_014222
Software, algorithmPyMOLThe PyMOL Molecular Graphics System, version 1.8 Schrödinger, LLC.https://pymol.org/2/#products; RRID:SCR_000305
Software, algorithmPDBePISAKrissinel and Henrick, 2007https://www.ebi.ac.uk/pdbe/pisa/; RRID:SCR_015749
Software, algorithmStrideHeinig and Frishman, 2004http://webclu.bio.wzw.tum.de/stride/
OtherHomemade
holey gold grids
Marr et al., 2014N/A
OtherHomemade
carbon grids
Booth et al., 2011N/A

Additional files

Supplementary file 1

Summary of CSP-derived peptides used in this study.

https://cdn.elifesciences.org/articles/72908/elife-72908-supp1-v2.docx
Supplementary file 2

Intramolecular H-bonds (3.0 A cutoff) in PvCSP peptides observed in Fab-peptide co-crystal structures.

No intramolecular H-bonds were detected for peptide 247-4.

https://cdn.elifesciences.org/articles/72908/elife-72908-supp2-v2.docx
Transparent reporting form
https://cdn.elifesciences.org/articles/72908/elife-72908-transrepform1-v2.pdf

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  1. Iga Kucharska
  2. Lamia Hossain
  3. Danton Ivanochko
  4. Qiren Yang
  5. John L Rubinstein
  6. Régis Pomès
  7. Jean-Philippe Julien
(2022)
Structural basis of Plasmodium vivax inhibition by antibodies binding to the circumsporozoite protein repeats
eLife 11:e72908.
https://doi.org/10.7554/eLife.72908