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- PDB-6bpb: Plasmodium vivax invasion blocking monoclonal antibody 4F7 -

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Basic information

Entry
Database: PDB / ID: 6bpb
TitlePlasmodium vivax invasion blocking monoclonal antibody 4F7
Components
  • Monoclonal antibody 4F7 Fab heavy chain
  • Monoclonal antibody 4F7 Fab light chain
KeywordsIMMUNE SYSTEM / Plasmodium vivax / invasion / malaria / antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsGruszczyk, J. / Chan, L.J. / Tham, W.H.
CitationJournal: Nature / Year: 2018
Title: Cryo-EM structure of an essential Plasmodium vivax invasion complex.
Authors: Jakub Gruszczyk / Rick K Huang / Li-Jin Chan / Sébastien Menant / Chuan Hong / James M Murphy / Yee-Foong Mok / Michael D W Griffin / Richard D Pearson / Wilson Wong / Alan F Cowman / ...Authors: Jakub Gruszczyk / Rick K Huang / Li-Jin Chan / Sébastien Menant / Chuan Hong / James M Murphy / Yee-Foong Mok / Michael D W Griffin / Richard D Pearson / Wilson Wong / Alan F Cowman / Zhiheng Yu / Wai-Hong Tham /
Abstract: Plasmodium vivax is the most widely distributed malaria parasite that infects humans. P. vivax invades reticulocytes exclusively, and successful entry depends on specific interactions between the P. ...Plasmodium vivax is the most widely distributed malaria parasite that infects humans. P. vivax invades reticulocytes exclusively, and successful entry depends on specific interactions between the P. vivax reticulocyte-binding protein 2b (PvRBP2b) and transferrin receptor 1 (TfR1). TfR1-deficient erythroid cells are refractory to invasion by P. vivax, and anti-PvRBP2b monoclonal antibodies inhibit reticulocyte binding and block P. vivax invasion in field isolates. Here we report a high-resolution cryo-electron microscopy structure of a ternary complex of PvRBP2b bound to human TfR1 and transferrin, at 3.7 Å resolution. Mutational analyses show that PvRBP2b residues involved in complex formation are conserved; this suggests that antigens could be designed that act across P. vivax strains. Functional analyses of TfR1 highlight how P. vivax hijacks TfR1, an essential housekeeping protein, by binding to sites that govern host specificity, without affecting its cellular function of transporting iron. Crystal and solution structures of PvRBP2b in complex with antibody fragments characterize the inhibitory epitopes. Our results establish a structural framework for understanding how P. vivax reticulocyte-binding protein engages its receptor and the molecular mechanism of inhibitory monoclonal antibodies, providing important information for the design of novel vaccine candidates.
History
DepositionNov 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2018Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_DOI
Revision 1.2Jul 11, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Jul 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Monoclonal antibody 4F7 Fab heavy chain
B: Monoclonal antibody 4F7 Fab light chain


Theoretical massNumber of molelcules
Total (without water)53,7472
Polymers53,7472
Non-polymers00
Water6,251347
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-24 kcal/mol
Surface area19160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.720, 63.340, 182.640
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Antibody Monoclonal antibody 4F7 Fab heavy chain


Mass: 27428.127 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody Monoclonal antibody 4F7 Fab light chain


Mass: 26319.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 347 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.86 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 20% (w/v) PEG 4,000, 0.05 M sodium citrate/citric acid, 20% (v/v) 2-propanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.87→43.89 Å / Num. obs: 34810 / % possible obs: 86.9 % / Redundancy: 5.6 % / CC1/2: 0.994 / Net I/σ(I): 7.7
Reflection shellResolution: 1.87→1.91 Å / Redundancy: 6 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2179 / CC1/2: 0.545 / % possible all: 85.7

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Processing

Software
NameVersionClassification
Blu-Icedata collection
iMOSFLM7.2.1data reduction
Aimless0.2.7data scaling
PHENIX1.11.1_2575phasing
PHENIX1.11.1_2575model building
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EN2

5en2


Resolution: 1.87→43.89 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.25
RfactorNum. reflection% reflection
Rfree0.2189 901 2.59 %
Rwork0.2062 --
obs0.2065 34753 86.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 101.08 Å2 / Biso mean: 38.8602 Å2 / Biso min: 17.29 Å2
Refinement stepCycle: final / Resolution: 1.87→43.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3239 0 0 347 3586
Biso mean---42.59 -
Num. residues----421
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043318
X-RAY DIFFRACTIONf_angle_d0.6514515
X-RAY DIFFRACTIONf_chiral_restr0.047507
X-RAY DIFFRACTIONf_plane_restr0.004572
X-RAY DIFFRACTIONf_dihedral_angle_d3.2731961
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8701-1.98730.34471200.29175444556485
1.9873-2.14070.26991620.24585373553584
2.1407-2.35610.27521320.24255324545683
2.3561-2.6970.2571150.22915337545282
2.697-3.39780.22881710.20835645581687
3.3978-43.90460.17872010.17516729693099
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
19.5601-3.5209-5.40452.5152.09857.08180.036-0.8504-1.12460.9421-0.071-0.26640.25781.0238-0.00190.3994-0.03080.00470.6055-0.1350.43139.543646.314168.8753
29.377-0.85614.97575.5657-3.88144.78940.6003-0.99640.4079-0.2822-0.11750.4709-0.5391-0.2753-0.55860.42910.160.12020.429-0.05130.295518.290550.294473.0819
32.3046-1.17751.92922.6085-0.05352.69850.2225-0.28830.76160.3997-0.1088-0.1824-0.54620.3362-0.02250.3982-0.09240.1360.3346-0.10820.409537.638951.84662.1817
47.29496.54793.92876.63641.10399.9103-0.16030.4842-1.4819-0.9370.25882.10952.7214-1.9386-0.03380.6977-0.18560.13940.3701-0.04910.899123.405936.876660.6638
54.55632.72464.10647.89592.47173.871-0.0330.39030.6771-0.48080.06590.2522-0.40050.0122-0.13250.3294-0.02290.17410.2777-0.01510.310130.11349.913755.3347
66.95923.3348-3.64676.3997-2.95682.52770.63640.80031.3823-0.46830.15910.5004-1.0228-0.3111-0.8810.64480.06680.22740.41170.0350.396628.538656.811754.0223
74.06940.6021.61663.7873-0.5525.99150.0592-0.85970.8038-0.0530.2704-0.4009-1.71740.0725-0.21350.6837-0.0310.21450.3597-0.1450.430132.782757.198464.0441
83.2583-2.1268-3.74122.33561.04677.0263-0.0438-0.18450.2028-0.08270.136-0.1309-0.3985-0.0989-0.02060.23820.04650.06060.24-0.00190.284230.292145.776861.9093
95.4047-2.8693.49317.3885-6.04715.3734-0.2982-0.23590.10870.10730.51320.5741-0.3601-1.7739-0.24710.26950.1280.02240.59970.05010.277913.878142.530878.683
105.0612-2.6745-0.84313.9720.28173.4933-0.16250.3999-0.28050.5397-0.04960.13710.2877-0.02790.11680.1562-0.02440.01230.294-0.04120.230123.156818.078484.9976
110.3313-0.2089-0.23287.8852-1.16550.40580.23160.23650.0989-0.3258-0.24350.14150.0357-0.01310.0310.20050.06120.01490.3311-0.03210.2421.108629.943979.6565
122.48542.5198-2.80556.5166-3.0834.11720.2197-0.1689-0.5028-0.0804-0.4987-0.7327-0.26010.1850.08670.1870.0448-0.01460.3131-0.13490.280433.453924.62784.013
133.0858-0.3764-0.6877.4667-0.57614.10290.3617-0.1782-0.0007-0.6825-0.01650.30660.1475-0.6499-0.08250.1413-0.01110.01970.427-0.09920.140823.345325.074674.9488
141.0576-1.2111-0.21664.8596-1.25142.88020.0819-0.1204-0.134-0.0385-0.1537-0.09020.20740.02850.10410.1220.00510.00650.2924-0.06430.251828.579918.961284.4771
152.3181-1.53820.59315.7982-2.87113.6306-0.0718-0.1510.4132-0.0471-0.0113-0.467-0.0543-0.15060.02520.20580.0055-0.00270.2624-0.08310.245525.142334.41586.2824
167.73973.9293-1.26914.1076-3.81495.84470.1776-1.4693-0.15030.8898-0.17650.81450.1154-1.08040.09770.3228-0.0430.01140.4706-0.00710.308124.116915.662692.5671
174.3496-0.13490.66796.4077-6.05197.8753-0.43070.1878-0.6031-0.43460.13941.21651.0589-0.04820.34360.485-0.02340.1830.4402-0.06240.426925.819232.191748.1797
185.9982-4.8462.85948.4206-1.50173.3628-0.165-0.2392-0.10510.46910.03210.4350.19060.00030.25510.5185-0.02170.22510.2959-0.05540.372135.889722.022548.3137
196.44581.7779-0.37799.49021.32553.31360.24360.32030.6158-1.7128-0.52130.3004-0.94880.46070.16460.64230.01270.04030.3110.05390.329930.249240.947738.8972
205.2662-1.10232.47817.5425-1.4617.8466-0.41240.0306-0.43290.3570.3878-0.263-0.3736-0.2868-0.13270.25490.0010.16430.1608-0.01870.364936.194835.745153.0413
215.84724.26251.93452.0098-3.21529.187-0.1514-0.0341-0.73280.47410.646-0.394-0.14821.0071-0.47160.32990.14530.0550.35630.01340.337339.600936.278256.7549
221.273-0.11-1.95622.65410.7855.19160.0352-0.1228-0.0938-0.5380.0896-0.60940.20460.4620.00530.40920.02010.24070.3534-0.05640.458742.091533.277946.3774
236.75152.0546-2.08344.1209-1.00760.6897-0.1766-0.25360.94620.4556-0.3197-0.5019-1.4827-0.9170.21010.80410.11410.08140.5411-0.15820.477641.719920.569456.3868
243.3467-0.60621.05291.91630.23740.4339-0.278-1.7062-0.50990.41530.1416-0.41860.3173-0.2303-0.19490.45240.09020.18170.70360.1590.467334.03329.343757.4649
252.4172-2.2878-1.75943.85022.81782.0622-0.15850.33660.1208-0.4059-0.016-0.18230.1455-0.2429-0.04130.31120.00150.11010.40810.02530.258230.451841.158349.0896
262.15560.2115-0.7641.1513-2.06813.7217-0.00320.10890.0537-0.18240.5786-0.1242-0.385-0.56861.39620.3858-0.1660.72420.4382-0.12520.416533.291215.0357.5494
275.6029-2.2279-3.75773.74991.80325.5698-0.0324-0.09150.04490.05930.0590.09740.40730.0334-0.06340.18670.0037-0.02050.2581-0.09340.240818.07115.092180.1187
286.17660.0888-5.66241.9247-0.48785.4501-0.38850.88160.1254-0.7030.360.22750.6222-0.68770.25340.3925-0.0324-0.00270.3473-0.1440.29117.40510.826868.1039
298.9182.3683-3.46023.10023.00358.34730.67261.2026-0.3421-1.301-0.30990.6732-0.421-0.8524-0.40680.36340.0028-0.14290.7285-0.0650.46614.349313.029272.4339
304.36530.9788-2.38052.6829-0.37344.97150.15430.10480.5075-0.46130.3481-0.1392-0.02170.2465-0.34780.22990.0330.00510.3571-0.06940.224720.547718.63771.4915
314.9949-5.7553-5.75717.40856.29997.2393-0.0365-0.4461-0.25010.2270.02190.49120.2050.0107-0.00870.1938-0.00210.01490.34230.01640.4184.093311.803484.6134
327.5826-1.7399-2.71854.5841.44573.9586-0.72760.5779-0.5187-0.20910.28760.50520.92070.08330.64320.4737-0.04480.05140.232-0.10360.365515.8775.048773.6904
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 20:27)A20 - 27
2X-RAY DIFFRACTION2(chain A and resid 28:36)A28 - 36
3X-RAY DIFFRACTION3(chain A and resid 37:57)A37 - 57
4X-RAY DIFFRACTION4(chain A and resid 58:63)A58 - 63
5X-RAY DIFFRACTION5(chain A and resid 64:71)A64 - 71
6X-RAY DIFFRACTION6(chain A and resid 72:85)A72 - 85
7X-RAY DIFFRACTION7(chain A and resid 86:102)A86 - 102
8X-RAY DIFFRACTION8(chain A and resid 103:135)A103 - 135
9X-RAY DIFFRACTION9(chain A and resid 136:141)A136 - 141
10X-RAY DIFFRACTION10(chain A and resid 142:161)A142 - 161
11X-RAY DIFFRACTION11(chain A and resid 162:175)A162 - 175
12X-RAY DIFFRACTION12(chain A and resid 176:182)A176 - 182
13X-RAY DIFFRACTION13(chain A and resid 183:197)A183 - 197
14X-RAY DIFFRACTION14(chain A and resid 198:221)A198 - 221
15X-RAY DIFFRACTION15(chain A and resid 222:232)A222 - 232
16X-RAY DIFFRACTION16(chain A and resid 233:237)A233 - 237
17X-RAY DIFFRACTION17(chain B and resid 24:35)B24 - 35
18X-RAY DIFFRACTION18(chain B and resid 36:48)B36 - 48
19X-RAY DIFFRACTION19(chain B and resid 49:55)B49 - 55
20X-RAY DIFFRACTION20(chain B and resid 56:63)B56 - 63
21X-RAY DIFFRACTION21(chain B and resid 67:72)B67 - 72
22X-RAY DIFFRACTION22(chain B and resid 73:99)B73 - 99
23X-RAY DIFFRACTION23(chain B and resid 100:105)B100 - 105
24X-RAY DIFFRACTION24(chain B and resid 106:110)B106 - 110
25X-RAY DIFFRACTION25(chain B and resid 111:126)B111 - 126
26X-RAY DIFFRACTION26(chain B and resid 127:131)B127 - 131
27X-RAY DIFFRACTION27(chain B and resid 132:160)B132 - 160
28X-RAY DIFFRACTION28(chain B and resid 161:174)B161 - 174
29X-RAY DIFFRACTION29(chain B and resid 175:181)B175 - 181
30X-RAY DIFFRACTION30(chain B and resid 182:207)B182 - 207
31X-RAY DIFFRACTION31(chain B and resid 208:215)B208 - 215
32X-RAY DIFFRACTION32(chain B and resid 216:235)B216 - 235

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