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- PDB-6bpd: Plasmodium vivax invasion blocking monoclonal antibody 10B12 -

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Basic information

Entry
Database: PDB / ID: 6bpd
TitlePlasmodium vivax invasion blocking monoclonal antibody 10B12
Components
  • Monoclonal antibody 10B12 Fab heavy chain
  • Monoclonal antibody 10B12 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: 2.32 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 10B12 Fab heavy chain
B: Monoclonal antibody 10B12 Fab light chain


Theoretical massNumber of molelcules
Total (without water)52,1822
Polymers52,1822
Non-polymers00
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-20 kcal/mol
Surface area18890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.540, 42.660, 105.034
Angle α, β, γ (deg.)90.000, 122.030, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody Monoclonal antibody 10B12 Fab heavy chain


Mass: 25463.381 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody Monoclonal antibody 10B12 Fab light chain


Mass: 26718.990 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.: 178 / 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: 2.16 Å3/Da / Density % sol: 42.98 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 20% (w/v) PEG 4,000, 0.1 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: 2.32→50.25 Å / Num. obs: 19567 / % possible obs: 99.5 % / Redundancy: 3.5 % / CC1/2: 0.992 / Net I/σ(I): 8.5
Reflection shellResolution: 2.32→2.4 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1882 / CC1/2: 0.539 / % possible all: 98.8

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Processing

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

5en2


Resolution: 2.32→44.525 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 28.03
RfactorNum. reflection% reflection
Rfree0.2619 935 5.13 %
Rwork0.2108 --
obs0.2136 18236 92.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 105.16 Å2 / Biso mean: 40.7956 Å2 / Biso min: 10.6 Å2
Refinement stepCycle: final / Resolution: 2.32→44.525 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3056 0 0 178 3234
Biso mean---35.35 -
Num. residues----397
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063134
X-RAY DIFFRACTIONf_angle_d0.9944266
X-RAY DIFFRACTIONf_chiral_restr0.052484
X-RAY DIFFRACTIONf_plane_restr0.005533
X-RAY DIFFRACTIONf_dihedral_angle_d5.5621836
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.32-2.44230.35421130.29942154226782
2.4423-2.59530.35491040.28262274237886
2.5953-2.79570.33621390.26042380251991
2.7957-3.0770.29561360.24252511264794
3.077-3.5220.27191350.20552634276998
3.522-4.43680.22131560.17092606276299
4.4368-44.5330.2141520.17952742289499
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)
14.32742.53821.87712.8103-0.19115.3004-0.0089-0.38451.32060.96030.08080.3795-0.0487-0.4727-0.14610.3556-0.0076-0.0390.13210.07010.3992-7.733119.913139.2556
21.86280.0413-1.3061.6422-0.62841.68630.0914-0.08520.24420.04680.15430.2707-0.3814-0.342-0.1880.35660.04760.0180.1322-0.04120.2379-7.946315.192345.6858
36.71471.88810.49574.6955-1.1065.18080.06580.9601-0.195-0.4952-0.0187-0.0855-0.03670.0657-0.18950.2084-0.0075-0.01490.1887-0.08080.2046-7.2254.688237.5172
42.86090.3149-0.72462.53910.11942.80950.1483-0.33670.0170.10410.144-0.10150.10280.1138-0.14930.23990.02910.03250.14880.03090.2003-9.6845.526250.2276
56.4656-2.0461-2.68962.82971.16692.1542-0.1040.02320.09010.7559-0.1310.10730.20040.05720.06270.18680.08860.09210.02730.08340.2626-3.917113.100648.6091
65.8705-2.11020.56195.39341.07433.9435-0.25480.2202-0.4022-0.44790.3230.2596-0.0746-0.04150.00530.2751-0.0728-0.00880.08870.01730.1754-2.9458.532637.6652
73.22852.6408-4.133.5643-1.60878.5367-0.05820.31461.12510.70240.74070.8857-0.455-2.0503-0.03760.4290.06-0.10350.59450.07640.4355-13.021315.468135.7385
81.8027-0.4495-1.64650.85410.90572.4171-0.22630.188-0.4053-0.31170.0905-0.19060.06620.07350.18630.2259-0.06280.02220.2415-0.0150.196115.320514.872327.9697
90.91930.2446-0.87010.6941.09627.73290.02450.0476-0.0383-0.5620.08740.2616-0.5380.2145-0.0160.51110.0126-0.00720.21770.03070.174313.915617.268618.698
102.4288-0.84630.92133.84681.32376.2380.0396-0.145-0.0314-0.39490.12570.1208-0.1258-0.8511-0.16640.2985-0.0211-0.01760.21760.0030.23811.010613.270519.8342
117.5363.95-3.17118.45680.34671.97670.35241.18310.2372-0.7260.1944-0.42750.1246-0.1452-0.29390.9613-0.10550.06460.39320.05060.410815.637520.20261.9193
121.5840.65471.38711.0432-0.09891.9856-0.04810.20160.2563-0.73730.5397-0.1755-0.96750.2924-0.07330.6425-0.0560.06510.23110.06880.338718.760323.64119.0554
132.7453-1.1713-0.51352.9234-0.43352.337-0.03030.6279-0.0147-0.1455-0.3177-0.33650.52660.26110.2240.30160.0237-0.05240.473-0.07630.3591-11.9862-1.777521.7065
143.7528-0.911.42364.5688-2.26036.88760.65890.1525-0.4389-0.1550.39060.75610.8944-0.8759-0.45990.4423-0.0834-0.13460.36290.00750.3779-21.2461-3.507828.6075
154.2699-0.7119-0.53295.89463.58782.68250.4672-0.65721.1491-0.2438-0.44940.6191-1.4483-0.26780.23730.6104-0.146-0.1070.7333-0.06340.8029-14.817411.668229.6853
166.14211.7476-3.37219.2308-3.99975.54990.69160.25930.3983-0.1552-0.41291.6959-0.4405-0.4226-0.73390.55710.0286-0.11420.68810.2720.5222-26.58874.970828.2724
177.13572.2146-0.43264.4023-0.6856.26020.54540.82920.8048-0.0130.65560.7644-0.1079-0.9307-0.67340.43420.0791-0.00610.51190.07710.3973-21.67313.941419.3192
183.6593-1.5672.28433.06231.86214.73870.25090.0946-0.2169-0.29040.05310.01370.4952-0.108-0.25410.2559-0.0188-0.00420.1607-0.00460.2858-14.419-0.275331.4843
195.11220.32150.94221.51350.65352.63760.3661-0.153-0.55420.02490.0002-0.34990.3494-0.3053-0.36830.3985-0.0697-0.07760.3028-0.00540.191310.51316.015911.1086
205.7955-1.3722-2.54669.35551.68312.936-0.16460.2507-1.38150.3277-0.0358-1.35411.01050.1312-0.34560.841-0.0142-0.25290.2264-0.11830.810318.0573-5.919613.1808
214.79270.27170.88444.67190.91073.41090.0247-0.34880.31610.7012-0.2527-0.1226-0.1075-0.22850.04140.412-0.14210.10370.3313-0.03350.20535.24565.2515.0857
221.00380.10380.1743.0129-0.31333.80440.2922-0.3056-0.46390.5580.0985-1.10521.13870.5734-0.41740.67650.2433-0.30270.338-0.05170.695423.07251.507418.3685
231.56351.137-0.00851.26340.55241.19850.00320.4813-0.4185-0.39150.2856-0.95230.07130.499-0.64581.01760.1174-0.442-0.1464-0.79860.396320.9712-2.99110.1876
245.15440.95420.81112.5049-0.03583.5730.17210.0747-1.2122-0.02620.3891-0.48340.41960.1999-0.51120.551-0-0.09220.2987-0.09690.395412.434-2.64945.26
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 21:29)A21 - 29
2X-RAY DIFFRACTION2(chain A and resid 30:53)A30 - 53
3X-RAY DIFFRACTION3(chain A and resid 54:69)A54 - 69
4X-RAY DIFFRACTION4(chain A and resid 70:92)A70 - 92
5X-RAY DIFFRACTION5(chain A and resid 93:106)A93 - 106
6X-RAY DIFFRACTION6(chain A and resid 107:117)A107 - 117
7X-RAY DIFFRACTION7(chain A and resid 127:131)A127 - 131
8X-RAY DIFFRACTION8(chain A and resid 132:151)A132 - 151
9X-RAY DIFFRACTION9(chain A and resid 160:179)A160 - 179
10X-RAY DIFFRACTION10(chain A and resid 180:206)A180 - 206
11X-RAY DIFFRACTION11(chain A and resid 207:218)A207 - 218
12X-RAY DIFFRACTION12(chain A and resid 219:236)A219 - 236
13X-RAY DIFFRACTION13(chain B and resid 20:35)B20 - 35
14X-RAY DIFFRACTION14(chain B and resid 36:62)B36 - 62
15X-RAY DIFFRACTION15(chain B and resid 63:74)B63 - 74
16X-RAY DIFFRACTION16(chain B and resid 75:83)B75 - 83
17X-RAY DIFFRACTION17(chain B and resid 84:110)B84 - 110
18X-RAY DIFFRACTION18(chain B and resid 111:129)B111 - 129
19X-RAY DIFFRACTION19(chain B and resid 130:170)B130 - 170
20X-RAY DIFFRACTION20(chain B and resid 171:178)B171 - 178
21X-RAY DIFFRACTION21(chain B and resid 179:198)B179 - 198
22X-RAY DIFFRACTION22(chain B and resid 199:214)B199 - 214
23X-RAY DIFFRACTION23(chain B and resid 215:220)B215 - 220
24X-RAY DIFFRACTION24(chain B and resid 221:236)B221 - 236

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