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- PDB-7cho: Crystal structure of SARS-CoV-2 antibody P5A-1D2 with RBD -

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Basic information

Entry
Database: PDB / ID: 7cho
TitleCrystal structure of SARS-CoV-2 antibody P5A-1D2 with RBD
Components
  • Spike protein S1
  • antibody P5A-1D2 heavy chain
  • antibody P5A-1D2 light chain
KeywordsVIRAL PROTEIN / spike / receptor binding domain / antibody
Function / homology
Function and homology information


Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / membrane fusion / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / receptor ligand activity / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.561 Å
AuthorsWang, X. / Zhang, L. / Ge, J. / Wang, R. / Zhang, Q.
CitationJournal: Nat Commun / Year: 2021
Title: Potent and protective IGHV3-53/3-66 public antibodies and their shared escape mutant on the spike of SARS-CoV-2.
Authors: Zhang, Q. / Ju, B. / Ge, J. / Chan, J.F. / Cheng, L. / Wang, R. / Huang, W. / Fang, M. / Chen, P. / Zhou, B. / Song, S. / Shan, S. / Yan, B. / Zhang, S. / Ge, X. / Yu, J. / Zhao, J. / Wang, ...Authors: Zhang, Q. / Ju, B. / Ge, J. / Chan, J.F. / Cheng, L. / Wang, R. / Huang, W. / Fang, M. / Chen, P. / Zhou, B. / Song, S. / Shan, S. / Yan, B. / Zhang, S. / Ge, X. / Yu, J. / Zhao, J. / Wang, H. / Liu, L. / Lv, Q. / Fu, L. / Shi, X. / Yuen, K.Y. / Liu, L. / Wang, Y. / Chen, Z. / Zhang, L. / Wang, X. / Zhang, Z.
History
DepositionJul 6, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 1, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Spike protein S1
H: antibody P5A-1D2 heavy chain
L: antibody P5A-1D2 light chain
A: Spike protein S1
B: antibody P5A-1D2 heavy chain
C: antibody P5A-1D2 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,0468
Polymers141,6046
Non-polymers4422
Water1,74797
1
E: Spike protein S1
H: antibody P5A-1D2 heavy chain
L: antibody P5A-1D2 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,0234
Polymers70,8023
Non-polymers2211
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Spike protein S1
B: antibody P5A-1D2 heavy chain
C: antibody P5A-1D2 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,0234
Polymers70,8023
Non-polymers2211
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)158.754, 67.509, 154.368
Angle α, β, γ (deg.)90.000, 112.180, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Spike protein S1 / S glycoprotein / E2 / Peplomer protein


Mass: 24600.631 Da / Num. of mol.: 2 / Fragment: receptor binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P0DTC2
#2: Antibody antibody P5A-1D2 heavy chain


Mass: 23475.209 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 antibody P5A-1D2 light chain


Mass: 22726.107 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: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.8 Å3/Da / Density % sol: 56.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2M Magnesium chloride hexahydrate, 0.1M Tris, pH 8.5, 3.4M 1,6-Hexanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9796 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.56→50 Å / Num. obs: 47159 / % possible obs: 95.9 % / Redundancy: 6.3 % / CC1/2: 0.989 / Rmerge(I) obs: 0.117 / Net I/σ(I): 9.5
Reflection shellResolution: 2.6→2.66 Å / Rmerge(I) obs: 0.799 / Num. unique obs: 3117 / CC1/2: 0.45

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6M0J

6m0j


Resolution: 2.561→36.523 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2473 2391 5.07 %
Rwork0.2017 44744 -
obs0.204 47135 95.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 130.68 Å2 / Biso mean: 54.0432 Å2 / Biso min: 25.97 Å2
Refinement stepCycle: final / Resolution: 2.561→36.523 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9429 0 28 97 9554
Biso mean--115.29 49.87 -
Num. residues----1247
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.561-2.61330.3564760.3299140451
2.6133-2.67010.39241130.3223231286
2.6701-2.73220.33661600.299259396
2.7322-2.80050.32251390.28872759100
2.8005-2.87620.31161380.26822698100
2.8762-2.96080.31661480.25632728100
2.9608-3.05630.29971380.25282729100
3.0563-3.16550.30551350.24222718100
3.1655-3.29210.28011490.23162747100
3.2921-3.44190.30041510.22242728100
3.4419-3.62320.26481410.20462725100
3.6232-3.84990.24081450.18952718100
3.8499-4.14680.23981650.17542746100
4.1468-4.56340.1661510.14912761100
4.5634-5.22210.19271410.15062755100
5.2221-6.57310.21241410.18712791100
6.5731-36.5230.22561600.1835283299

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