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- PDB-6rcv: PfRH5 bound to monoclonal antibodies R5.011 and R5.016 -

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Open data


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Basic information

Entry
Database: PDB / ID: 6rcv
TitlePfRH5 bound to monoclonal antibodies R5.011 and R5.016
Components
  • R5.011 heavy chain
  • R5.011 light chain
  • R5.016 heavy chain
  • R5.016 light chain
  • Reticulocyte binding protein homologue 5
KeywordsCELL ADHESION / Plasmodium falciparum Erythrocyte invasion Potentiating antibody Neutralising antibody Human monoclonal antibody
Function / homology
Function and homology information


rhoptry lumen / rhoptry / symbiont entry into host / bicellular tight junction / host cell membrane / apical part of cell / heparin binding / cytoplasmic vesicle / host extracellular space / host cell surface receptor binding ...rhoptry lumen / rhoptry / symbiont entry into host / bicellular tight junction / host cell membrane / apical part of cell / heparin binding / cytoplasmic vesicle / host extracellular space / host cell surface receptor binding / host cell plasma membrane / protein-containing complex / extracellular region / membrane
Similarity search - Function
Rh5 coiled-coil domain / Rh5 coiled-coil domain / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Reticulocyte-binding protein homolog 5
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.582 Å
AuthorsAlanine, D.W.G. / Draper, S.J. / Higgins, M.K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: Cell / Year: 2019
Title: Human Antibodies that Slow Erythrocyte Invasion Potentiate Malaria-Neutralizing Antibodies.
Authors: Alanine, D.G.W. / Quinkert, D. / Kumarasingha, R. / Mehmood, S. / Donnellan, F.R. / Minkah, N.K. / Dadonaite, B. / Diouf, A. / Galaway, F. / Silk, S.E. / Jamwal, A. / Marshall, J.M. / Miura, ...Authors: Alanine, D.G.W. / Quinkert, D. / Kumarasingha, R. / Mehmood, S. / Donnellan, F.R. / Minkah, N.K. / Dadonaite, B. / Diouf, A. / Galaway, F. / Silk, S.E. / Jamwal, A. / Marshall, J.M. / Miura, K. / Foquet, L. / Elias, S.C. / Labbe, G.M. / Douglas, A.D. / Jin, J. / Payne, R.O. / Illingworth, J.J. / Pattinson, D.J. / Pulido, D. / Williams, B.G. / de Jongh, W.A. / Wright, G.J. / Kappe, S.H.I. / Robinson, C.V. / Long, C.A. / Crabb, B.S. / Gilson, P.R. / Higgins, M.K. / Draper, S.J.
History
DepositionApr 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev / database_PDB_rev_record
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Reticulocyte binding protein homologue 5
B: R5.011 light chain
C: R5.011 heavy chain
D: R5.016 light chain
E: R5.016 heavy chain
F: Reticulocyte binding protein homologue 5
G: R5.011 light chain
H: R5.011 heavy chain
I: R5.016 light chain
J: R5.016 heavy chain


Theoretical massNumber of molelcules
Total (without water)367,20310
Polymers367,20310
Non-polymers00
Water00
1
A: Reticulocyte binding protein homologue 5
D: R5.016 light chain
E: R5.016 heavy chain

B: R5.011 light chain
C: R5.011 heavy chain


Theoretical massNumber of molelcules
Total (without water)183,6015
Polymers183,6015
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_544-x+1/2,-y-1,z-1/21
Buried area11990 Å2
ΔGint-64 kcal/mol
Surface area53130 Å2
MethodPISA
2
F: Reticulocyte binding protein homologue 5
I: R5.016 light chain
J: R5.016 heavy chain

G: R5.011 light chain
H: R5.011 heavy chain


Theoretical massNumber of molelcules
Total (without water)183,6015
Polymers183,6015
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1/2,-y-1,z+1/21
Buried area11630 Å2
ΔGint-66 kcal/mol
Surface area53080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.994, 150.991, 163.974
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Reticulocyte binding protein homologue 5


Mass: 59993.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: PF3D7_0424100 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q8IFM5
#2: Antibody R5.011 light chain


Mass: 23065.367 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody R5.011 heavy chain


Mass: 25685.484 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody R5.016 light chain


Mass: 23953.613 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#5: Antibody R5.016 heavy chain


Mass: 50902.977 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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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: 2.38 Å3/Da / Density % sol: 48.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 10% PEG 20000, 20% PEG 550MME, 0.02 M amino acids, 0.1 M MES/imidazole pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.58→49.16 Å / Num. obs: 41777 / % possible obs: 99.7 % / Redundancy: 6.7 % / Net I/σ(I): 4.7
Reflection shellResolution: 3.58→3.73 Å / Num. unique obs: 4579

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.582→49.156 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.46
RfactorNum. reflection% reflection
Rfree0.3054 2037 4.91 %
Rwork0.2802 --
obs0.2815 41468 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.582→49.156 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18311 0 0 0 18311
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00918771
X-RAY DIFFRACTIONf_angle_d1.27725500
X-RAY DIFFRACTIONf_dihedral_angle_d23.2336816
X-RAY DIFFRACTIONf_chiral_restr0.2522833
X-RAY DIFFRACTIONf_plane_restr0.0073220
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5822-3.66550.40061310.38372524X-RAY DIFFRACTION97
3.6655-3.75720.35661490.35772563X-RAY DIFFRACTION99
3.7572-3.85870.34681660.32262565X-RAY DIFFRACTION99
3.8587-3.97220.31641440.3372601X-RAY DIFFRACTION100
3.9722-4.10040.35571320.31792596X-RAY DIFFRACTION99
4.1004-4.24680.3471230.28862620X-RAY DIFFRACTION99
4.2468-4.41680.30561210.27732626X-RAY DIFFRACTION99
4.4168-4.61770.29041120.26122629X-RAY DIFFRACTION99
4.6177-4.86090.29521110.25282661X-RAY DIFFRACTION100
4.8609-5.16520.25731450.25882634X-RAY DIFFRACTION100
5.1652-5.56350.31151200.26852655X-RAY DIFFRACTION100
5.5635-6.12240.35971380.26942646X-RAY DIFFRACTION100
6.1224-7.00610.29661150.29652697X-RAY DIFFRACTION100
7.0061-8.81870.30491200.25132730X-RAY DIFFRACTION100
8.8187-49.16030.23912100.22392684X-RAY DIFFRACTION97
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.96380.03120.96612.228-1.90654.9025-0.10890.09930.08080.01910.098-0.06070.12820.05930.03960.54160.12180.12330.6562-0.00890.390322.9651-71.2531-10.8609
23.0552-0.24550.16161.87411.58911.2470.5741-0.0582-1.120.2135-0.3657-0.37121.63830.3375-0.30371.06580.01920.06351.22540.15981.066817.3909-101.29194.6809
32.396-0.8881.11353.1821-0.02042.402-0.0902-0.2255-0.31630.15340.2277-0.39730.7371-0.0121-0.09920.69450.19650.11830.55760.03240.466415.4302-83.5318-6.5539
42.4863-0.88741.48990.58620.24635.9310.1963-0.0508-0.25510.0895-0.1622-0.5998-0.3506-0.328-0.01120.54470.03010.03050.81180.1060.358833.3894-72.402926.644
53.7203-0.8357-1.81571.72180.45441.38420.459-0.66220.8877-0.2873-0.27770.6512-1.803-0.8869-0.30451.28780.3743-0.10371.4625-0.09050.744618.2748-52.819166.0718
62.6243-1.062-1.14532.0163-1.00056.6280.0462-0.0057-0.43170.5337-0.4811.1762-0.2704-0.7490.46780.7460.1506-0.05721.2341-0.14810.561225.1995-65.741561.5522
71.34330.26330.2463.70761.82834.1777-0.271-0.6043-0.16530.5721-0.74260.4613-0.7082-1.34450.89130.87520.1826-0.14671.0838-0.19520.829723.2995-61.215861.0842
81.2142-0.36620.29042.51660.84651.5224-0.4816-0.77960.29110.76720.51870.2484-0.51020.3096-0.19930.9919-0.03570.01751.2728-0.00360.436829.613-64.410767.1499
94.767-0.57790.74291.3442-0.37214.9103-0.3111-0.5223-0.05620.04980.0915-0.0582-0.3178-0.81040.17350.56390.112-0.03020.8571-0.07150.411312.8283-61.070121.7481
101.13280.1560.75920.6122-0.07385.2372-0.3742-0.31250.39910.3861-0.0248-0.0482-1.1089-0.61430.41930.8910.2779-0.13860.91160.00020.733620.5928-57.755738.5786
115.91470.7028-1.91031.32011.50665.08810.8998-2.1271.4417-0.2794-0.5559-0.3275-1.22681.4413-0.2371.8937-0.0083-0.24781.519-0.30830.930430.8276-43.016660.7087
121.3232-0.2991.30152.9899-1.53221.8860.95671.03531.4962-0.2277-0.2942-0.0323-0.7927-0.7666-0.40421.62990.772-0.24451.61580.14510.847117.5854-42.672556.0932
135.4383-0.5166-0.55672.99471.57982.47781.1912-0.44611.240.5395-0.71210.0156-0.68150.5111-0.72591.0343-0.1250.18010.7323-0.06780.731944.7361-44.4528-21.4527
145.4861.37381.10223.49230.59926.26710.23390.1449-0.15420.3236-0.2278-0.33010.03490.641-0.00020.79850.01350.10670.7153-0.12570.583544.1576-53.4046-17.6065
152.9328-0.2427-1.96632.77540.38131.02360.4406-0.69060.96470.20780.0851-1.1166-0.55921.2056-0.5040.8636-0.28350.10491.469-0.1681.146872.696-48.1488-28.8582
162.2398-1.57551.3032.2211-2.06432.02981.38620.76430.0291-0.13720.47160.37710.21650.9438-1.17521.5536-0.33950.45171.7573-0.70091.519883.4317-40.6292-24.9826
174.54411.0726-1.41853.30970.47233.6482-0.16180.96870.2475-0.02420.3371-0.2101-0.4703-0.1753-0.20240.6510.04030.06320.9402-0.05610.357241.6739-64.2008-35.9521
184.42510.66030.91542.41221.38144.03730.34010.4145-0.06170.90730.3321-0.54490.39770.7862-0.52290.91810.1127-0.04870.99460.01991.002179.1066-62.5017-29.0281
191.7195-0.7140.57232.51493.64326.0228-0.0742-0.2140.13690.3516-0.0190.15540.1186-0.46290.0280.59510.07890.03610.84820.11730.3459-24.8947-71.4575-0.5122
203.09170.7644-0.50549.0342.31772.1021-0.29240.1405-0.3362-0.127-0.16362.5170.940.32070.60640.983-0.0809-0.04580.92080.04330.6345-35.9325-84.4161-18.5268
213.7432-0.5933-0.34061.8383-0.51540.3873-0.2199-0.122-0.38410.36930.162-0.02830.1967-0.07880.07120.7180.11020.06040.6883-0.08150.5251-14.1063-74.03252.5563
222.7508-3.420.9477.88481.07461.64460.16781.246-0.6496-0.09280.18180.48560.69490.0298-0.43142.5823-0.403-0.3220.41520.29081.7043-25.5623-109.3543-25.2783
233.01241.21680.42192.8640.25711.3943-0.01110.3174-0.5001-0.03070.1066-0.01070.352-0.3187-0.0320.68380.11810.07810.8454-0.05410.4425-15.169-83.3126-4.5787
242.11181.63940.54743.03081.9764.6504-0.15130.0731-0.0022-0.04760.00770.54190.13190.02930.06360.54850.12180.02660.88270.01450.4368-34.1963-72.8676-36.2568
251.98070.52991.58611.9679-1.25194.617-0.38710.04070.3499-0.59850.2956-0.09610.2508-0.1011-0.00220.5640.18860.06220.3906-0.03080.4286-26.2354-64.0326-62.4721
261.05863.0754-0.51828.7379-1.24683.3392-0.25710.55221.2842-1.5784-0.0432-1.45010.20180.2693-0.09860.7260.38750.11221.0761-0.01130.9556-19.4311-68.9437-77.2734
273.14650.92850.37092.79550.24113.2803-0.39260.3174-0.0949-0.77260.0675-0.07340.01430.03750.08520.76130.2517-0.07061.08920.03280.5201-23.3769-61.2195-72.2812
284.89992.1008-0.74927.1336-1.25186.4255-2.3930.3121-0.1846-0.83861.0296-1.01680.2364-0.18930.88010.73190.18540.08120.82370.00420.5425-30.0314-64.9276-77.8967
295.31471.7851-0.51242.6431-1.06123.791-0.26210.2638-0.00410.09460.022-0.22380.0588-0.37840.24750.56240.1817-0.09140.7899-0.02670.3723-15.6347-62.8721-31.8863
303.52860.711-0.33240.15360.14162.84250.57760.44931.56740.3347-0.86510.61120.31640.1940.04920.6971-0.0895-0.00340.77260.24951.0912-14.3895-51.5107-66.392
312.2210.8602-1.15934.25280.8214.3826-0.0707-0.20510.20810.08190.15650.2661-0.16890.5217-0.34740.7416-0.1094-0.15381.0180.17760.6173-20.885-51.7808-63.1537
323.6161-1.38841.68322.6312-1.0742.03720.24811.19581.6071-0.42410.10351.9506-1.8918-0.4001-0.07280.99490.277-0.30071.59360.4331.0205-31.3743-43.1081-71.7933
333.59510.6081-1.52222.48430.47890.86171.4767-0.09620.5306-0.6449-0.3866-0.67440.1246-0.1478-0.87851.4977-0.0769-0.01131.1292-0.00850.779-18.3249-42.5428-67.4655
345.69930.0930.26883.1876-1.14514.7033-0.05750.19060.6937-0.66520.23190.6843-0.4387-0.1444-0.27160.82890.3273-0.03030.74210.11550.7078-44.4535-50.33397.4583
351.8919-0.77880.3020.9728-0.67311.15560.2715-0.05970.9996-0.18790.33671.2145-0.3383-0.3368-0.69141.03250.37510.08851.23510.09761.7476-73.8877-47.287516.9674
365.6078-0.8901-2.11922.76020.12443.51380.1131-0.1710.418-0.01960.23170.3316-0.30510.0672-0.36160.63340.22790.00430.82050.05170.3856-40.9925-63.992124.6405
373.5976-0.5891-0.3764-0.0311-0.2750.98740.111-0.662-0.644-0.37990.34161.16880.4077-0.9525-0.30910.97670.0665-0.27311.39070.11551.5122-76.814-63.339118.7785
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 144 through 375 )
2X-RAY DIFFRACTION2chain 'A' and (resid 376 through 403 )
3X-RAY DIFFRACTION3chain 'A' and (resid 404 through 500 )
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 115 )
5X-RAY DIFFRACTION5chain 'B' and (resid 116 through 131 )
6X-RAY DIFFRACTION6chain 'B' and (resid 132 through 163 )
7X-RAY DIFFRACTION7chain 'B' and (resid 164 through 192 )
8X-RAY DIFFRACTION8chain 'B' and (resid 193 through 212 )
9X-RAY DIFFRACTION9chain 'C' and (resid 1 through 91 )
10X-RAY DIFFRACTION10chain 'C' and (resid 92 through 192 )
11X-RAY DIFFRACTION11chain 'C' and (resid 193 through 209 )
12X-RAY DIFFRACTION12chain 'C' and (resid 210 through 231 )
13X-RAY DIFFRACTION13chain 'D' and (resid 2 through 32 )
14X-RAY DIFFRACTION14chain 'D' and (resid 33 through 90 )
15X-RAY DIFFRACTION15chain 'D' and (resid 91 through 198 )
16X-RAY DIFFRACTION16chain 'D' and (resid 199 through 211 )
17X-RAY DIFFRACTION17chain 'E' and (resid 1 through 127 )
18X-RAY DIFFRACTION18chain 'E' and (resid 128 through 232 )
19X-RAY DIFFRACTION19chain 'F' and (resid 144 through 239 )
20X-RAY DIFFRACTION20chain 'F' and (resid 240 through 320 )
21X-RAY DIFFRACTION21chain 'F' and (resid 321 through 395 )
22X-RAY DIFFRACTION22chain 'F' and (resid 396 through 403 )
23X-RAY DIFFRACTION23chain 'F' and (resid 404 through 499 )
24X-RAY DIFFRACTION24chain 'G' and (resid 2 through 91 )
25X-RAY DIFFRACTION25chain 'G' and (resid 92 through 152 )
26X-RAY DIFFRACTION26chain 'G' and (resid 153 through 163 )
27X-RAY DIFFRACTION27chain 'G' and (resid 164 through 192 )
28X-RAY DIFFRACTION28chain 'G' and (resid 193 through 211 )
29X-RAY DIFFRACTION29chain 'H' and (resid 1 through 126 )
30X-RAY DIFFRACTION30chain 'H' and (resid 127 through 150 )
31X-RAY DIFFRACTION31chain 'H' and (resid 151 through 192 )
32X-RAY DIFFRACTION32chain 'H' and (resid 193 through 208 )
33X-RAY DIFFRACTION33chain 'H' and (resid 209 through 231 )
34X-RAY DIFFRACTION34chain 'I' and (resid 2 through 90 )
35X-RAY DIFFRACTION35chain 'I' and (resid 91 through 211 )
36X-RAY DIFFRACTION36chain 'J' and (resid 1 through 119 )
37X-RAY DIFFRACTION37chain 'J' and (resid 120 through 232 )

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  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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