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- PDB-6w7y: Crystal structure of SARS-CoV and SARS-CoV-2 reactive human antib... -

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Basic information

Entry
Database: PDB / ID: 6w7y
TitleCrystal structure of SARS-CoV and SARS-CoV-2 reactive human antibody CR3022
Components
  • CR3022 Heavy chain
  • CR3022 Light chain
KeywordsIMMUNE SYSTEM / Coronavirus / receptor-binding domain / COVID-19 / vaccine target / antibody / cryptic epitope / VIRAL PROTEIN
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsChen, W.H. / Joyce, M.G.
CitationJournal: To Be Published
Title: Structure and Antigenicity of the SARS-CoV-2 Receptor Binding Domain
Authors: Chen, W.H. / Joyce, M.G.
History
DepositionMar 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: CR3022 Heavy chain
L: CR3022 Light chain
A: CR3022 Heavy chain
B: CR3022 Light chain


Theoretical massNumber of molelcules
Total (without water)95,8954
Polymers95,8954
Non-polymers00
Water00
1
H: CR3022 Heavy chain
L: CR3022 Light chain


Theoretical massNumber of molelcules
Total (without water)47,9482
Polymers47,9482
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-25 kcal/mol
Surface area20260 Å2
MethodPISA
2
A: CR3022 Heavy chain
B: CR3022 Light chain


Theoretical massNumber of molelcules
Total (without water)47,9482
Polymers47,9482
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-22 kcal/mol
Surface area20070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.065, 201.032, 56.971
Angle α, β, γ (deg.)90.000, 109.440, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 15 or resid 17...
21(chain H and (resid 2 through 15 or resid 17...
12(chain B and (resid 1 or resid 3 through 105...
22(chain L and (resid 1 or resid 3 through 105...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 2 through 15 or resid 17...A2 - 15
121(chain A and (resid 2 through 15 or resid 17...A17 - 42
131(chain A and (resid 2 through 15 or resid 17...A1 - 221
141(chain A and (resid 2 through 15 or resid 17...A0
151(chain A and (resid 2 through 15 or resid 17...A60 - 66
161(chain A and (resid 2 through 15 or resid 17...A68 - 81
171(chain A and (resid 2 through 15 or resid 17...A83 - 219
211(chain H and (resid 2 through 15 or resid 17...H2 - 15
221(chain H and (resid 2 through 15 or resid 17...H17 - 42
231(chain H and (resid 2 through 15 or resid 17...H44 - 45
241(chain H and (resid 2 through 15 or resid 17...H48 - 56
251(chain H and (resid 2 through 15 or resid 17...H60 - 66
261(chain H and (resid 2 through 15 or resid 17...H68 - 81
271(chain H and (resid 2 through 15 or resid 17...H83 - 219
112(chain B and (resid 1 or resid 3 through 105...B1
122(chain B and (resid 1 or resid 3 through 105...B3 - 105
132(chain B and (resid 1 or resid 3 through 105...B107 - 112
142(chain B and (resid 1 or resid 3 through 105...B1 - 219
152(chain B and (resid 1 or resid 3 through 105...B165 - 170
162(chain B and (resid 1 or resid 3 through 105...B1
172(chain B and (resid 1 or resid 3 through 105...B8
182(chain B and (resid 1 or resid 3 through 105...B210 - 218
212(chain L and (resid 1 or resid 3 through 105...L1
222(chain L and (resid 1 or resid 3 through 105...L3 - 105
232(chain L and (resid 1 or resid 3 through 105...L107 - 112
242(chain L and (resid 1 or resid 3 through 105...L1 - 218
252(chain L and (resid 1 or resid 3 through 105...L165 - 170
262(chain L and (resid 1 or resid 3 through 105...L1
272(chain L and (resid 1 or resid 3 through 105...L8
282(chain L and (resid 1 or resid 3 through 105...L210 - 218

NCS ensembles :
ID
1
2

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Components

#1: Antibody CR3022 Heavy chain


Mass: 23668.609 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody CR3022 Light chain


Mass: 24278.924 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
Has protein modificationY

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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: 2.93 Å3/Da / Density % sol: 58.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M imidazole, pH 6.5, 40% 2-propanol, 15% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 25, 2020
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→53.72 Å / Num. obs: 16019 / % possible obs: 96.5 % / Redundancy: 1.9 % / CC1/2: 0.991 / Rpim(I) all: 0.063 / Net I/σ(I): 10.2
Reflection shellResolution: 3.3→3.42 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2430 / CC1/2: 0.935 / Rpim(I) all: 0.198

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5XS7

5xs7


Resolution: 3.3→53.72 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2783 800 5 %
Rwork0.2515 15199 -
obs0.2528 15999 96.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 145.74 Å2 / Biso mean: 72.7833 Å2 / Biso min: 37.64 Å2
Refinement stepCycle: final / Resolution: 3.3→53.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6583 0 0 0 6583
Num. residues----866
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1596X-RAY DIFFRACTION20.59TORSIONAL
12H1596X-RAY DIFFRACTION20.59TORSIONAL
21B1738X-RAY DIFFRACTION20.59TORSIONAL
22L1738X-RAY DIFFRACTION20.59TORSIONAL
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 (%)
3.3-3.510.35951280.3292430255893
3.51-3.780.33951350.29482569270499
3.78-4.160.31311360.29292576271299
4.16-4.760.24381350.2282582271797
4.76-5.990.26431310.232475260695
6-53.720.24121350.2132567270296
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)
12.92020.33920.92871.2324-1.23551.7313-0.4779-0.3411-0.76330.05260.80621.1425-0.1237-0.00230.16840.72330.12370.3070.5760.10850.6787-54.7206-37.9833-6.7043
21.544-2.1012-0.08863.9789-0.16360.24630.07710.10620.06391.21460.10990.2636-0.3353-0.28070.10820.76450.06690.15850.58390.03840.3679-47.885-37.1025-0.0176
3-0.08020.21110.41013.6421-1.38552.71340.0943-0.17220.1422-0.28590.14180.1730.17040.0990.05030.49710.1418-0.00280.47280.02860.3228-43.4103-16.956-28.5078
43.96380.122-0.98483.0353-0.24032.2749-0.1378-0.1752-0.20060.1249-0.1136-0.89330.34140.54330.06250.6820.11080.00690.43080.11150.5807-29.5985-46.7339-7.3698
52.87090.5279-0.15642.708-1.33761.482-0.2841-0.07110.1760.6645-0.2392-0.68690.1415-0.35440.06770.51650.08920.00770.54690.05920.4262-31.0716-43.1907-8.1097
62.953-0.7315-0.14753.2639-0.02421.00220.041-0.08090.31120.3652-0.27-0.5056-0.21490.0607-0.00820.56110.0386-0.00690.51350.09240.3513-27.6669-12.9277-24.7443
70.86930.1199-1.23643.11580.63751.80941.08970.4151-0.4932-0.2854-0.17060.0234-1.37980.1667-0.07940.7584-0.0762-0.12180.635-0.12480.6122-5.15922.845-3.9791
80.3096-0.65951.038.6434-0.95692.52670.7094-0.00560.3033-2.0461-0.0537-0.4342-0.24910.32260.18030.5993-0.0020.31550.6289-0.20710.92081.096725.9047-2.2987
92.4996-2.7287-1.47543.35091.25282.1150.2045-0.13890.3096-0.25390.3667-0.91390.33140.1612-0.14770.6854-0.02130.05520.5676-0.07420.91982.84222.68725.9441
100.24310.1066-0.16844.08780.2839-0.1559-0.0161-0.11120.0244-0.5066-0.01890.0005-0.03430.1311-0.11090.69440.052-0.10890.6138-0.09560.4112-14.83149.26810.8252
110.83220.1244-1.2991.13610.94482.3677-0.6215-0.0720.0564-0.40540.10190.2391-0.1717-0.2998-0.08380.68580.0638-0.25750.4951-0.03720.5904-24.37113.9374-1.2441
126.89722.41780.35872.7446-0.93891.2977-0.79412.2427-0.3677-0.86050.4581-0.3830.142-0.1805-0.23711.15620.021-0.57590.3846-0.22410.4433-31.46191.146-9.2085
131.8532-0.54830.64771.56480.67461.9002-0.1610.5855-0.9589-0.046-0.0336-0.239-0.7898-0.15490.00091.15740.0286-0.24870.5035-0.06780.659-24.9907-2.1757-9.9506
141.55620.66660.26152.15031.76871.5723-0.44540.4092-0.06441.70210.4208-0.5002-0.3190.196-0.10411.29430.0394-0.03450.4499-0.01250.5532-17.770424.853723.4287
150.588-0.17920.25230.9204-0.29331.41190.05480.5459-0.49340.52860.6551-0.7252-0.27991.2747-0.19610.7286-0.0565-0.19320.7132-0.06290.6242-6.356135.756621.5869
160.51710.5268-0.44562.59330.33680.77490.17590.2145-0.17521.27690.17990.55420.4312-0.0366-0.12210.83140.1259-0.01020.753-0.03630.6374-16.474233.866615.6776
173.35850.5842-1.22993.10790.22441.5741-0.3532-0.09580.34970.32560.2174-0.22660.39310.1451-0.11790.55520.1362-0.05830.6032-0.15490.5335-12.385827.587316.5784
182.0693-0.2889-0.28163.3037-1.39190.75890.03170.0477-0.2493-0.0792-0.24081.2026-0.08120.0065-0.00790.55720.0531-0.04680.5071-0.01630.5352-28.1489-0.314710.7564
191.29890.5249-0.84832.05040.48762.09210.2966-0.0488-0.418-0.6244-0.39350.6687-0.05370.2942-0.04820.6190.0391-0.15370.373-0.06170.5361-23.7821-3.286310.3722
202.4256-0.38540.1214.8929-0.70521.499-0.0454-0.2113-0.51040.577-0.9241.25670.4563-0.36660.14080.514-0.053-0.12660.46970.08460.6672-32.0487-9.451314.8595
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 32 )H1 - 32
2X-RAY DIFFRACTION2chain 'H' and (resid 33 through 112 )H33 - 112
3X-RAY DIFFRACTION3chain 'H' and (resid 113 through 220 )H113 - 220
4X-RAY DIFFRACTION4chain 'L' and (resid 1 through 76 )L1 - 76
5X-RAY DIFFRACTION5chain 'L' and (resid 77 through 108 )L77 - 108
6X-RAY DIFFRACTION6chain 'L' and (resid 109 through 218 )L109 - 218
7X-RAY DIFFRACTION7chain 'A' and (resid 1 through 12 )A1 - 12
8X-RAY DIFFRACTION8chain 'A' and (resid 13 through 32 )A13 - 32
9X-RAY DIFFRACTION9chain 'A' and (resid 33 through 99 )A33 - 99
10X-RAY DIFFRACTION10chain 'A' and (resid 100 through 151 )A100 - 151
11X-RAY DIFFRACTION11chain 'A' and (resid 152 through 194 )A152 - 194
12X-RAY DIFFRACTION12chain 'A' and (resid 195 through 206 )A195 - 206
13X-RAY DIFFRACTION13chain 'A' and (resid 207 through 221 )A207 - 221
14X-RAY DIFFRACTION14chain 'B' and (resid 1 through 24 )B1 - 24
15X-RAY DIFFRACTION15chain 'B' and (resid 25 through 44 )B25 - 44
16X-RAY DIFFRACTION16chain 'B' and (resid 45 through 81 )B45 - 81
17X-RAY DIFFRACTION17chain 'B' and (resid 82 through 108 )B82 - 108
18X-RAY DIFFRACTION18chain 'B' and (resid 109 through 156 )B109 - 156
19X-RAY DIFFRACTION19chain 'B' and (resid 157 through 194 )B157 - 194
20X-RAY DIFFRACTION20chain 'B' and (resid 195 through 219 )B195 - 219

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