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- PDB-7vmu: Crystal Structure of SARS-CoV Spike Receptor-Binding Domain Compl... -

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Basic information

Entry
Database: PDB / ID: 7vmu
TitleCrystal Structure of SARS-CoV Spike Receptor-Binding Domain Complexed with Neutralizing Antibody
Components
  • Spike protein S1
  • scFv E4
KeywordsIMMUNE SYSTEM / SARS-CoV-2 variants / COVID-19 / neutralizing antibody / phage display library / antibody engineering
Function / homology
Function and homology information


symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / viral translation / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion ...symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / viral translation / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / membrane fusion / entry receptor-mediated virion attachment to host cell / 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 / symbiont entry into host cell / 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, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / 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 (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, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / 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 / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2 superfamily, coronavirus / 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, coronavirus / Coronavirus spike glycoprotein S2 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsGuo, Y. / Wang, W. / Jiao, P. / Yang, H. / Rao, Z. / Cheng, G.
Funding support United States, 5items
OrganizationGrant numberCountry
Other government2019-I2M-5-049 United States
Other government2016-I2M-1-005 United States
Other government2019XK310002 United States
National Natural Science Foundation of China (NSFC)91542201, 81925025, 82102371 and 81802870 United States
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)R01AI069120, AI158154 and AI140718 United States
CitationJournal: Cell Biosci / Year: 2022
Title: Antibody engineering improves neutralization activity against K417 spike mutant SARS-CoV-2 variants.
Authors: Li, L. / Gao, M. / Jiao, P. / Zu, S. / Deng, Y.Q. / Wan, D. / Cao, Y. / Duan, J. / Aliyari, S.R. / Li, J. / Shi, Y. / Rao, Z. / Qin, C.F. / Guo, Y. / Cheng, G. / Yang, H.
History
DepositionOct 9, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 30, 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
A: scFv E4
B: Spike protein S1


Theoretical massNumber of molelcules
Total (without water)45,8912
Polymers45,8912
Non-polymers00
Water00
1
A: scFv E4

B: Spike protein S1


Theoretical massNumber of molelcules
Total (without water)45,8912
Polymers45,8912
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,-x,z+1/41
Buried area1490 Å2
ΔGint-10 kcal/mol
Surface area18060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.021, 97.021, 93.244
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322

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Components

#1: Antibody scFv E4


Mass: 25423.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Protein Spike protein S1


Mass: 20467.893 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: P0DTC2
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: 2.52 Å3/Da / Density % sol: 51.21 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 20% w/v PEG3350, 0.2M potassium citrate tribasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.89→50 Å / Num. obs: 9975 / % possible obs: 95.2 % / Redundancy: 10.3 % / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.047 / Rrim(I) all: 0.157 / Χ2: 0.888 / Net I/σ(I): 5.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.9-2.958.71.2414950.5580.4221.3150.72496.7
2.95-39.71.1654860.7260.3791.2280.71796
3-3.0610.40.8794980.8290.2740.9230.72696.9
3.06-3.1211.30.7884880.8710.2370.8240.72496.1
3.12-3.1911.10.6554870.8980.1980.6860.7597.8
3.19-3.2710.50.5925100.8920.1840.6211.15797.3
3.27-3.3510.40.4924940.9310.1540.5160.81595.9
3.35-3.4410.80.4394830.9520.1350.460.87997
3.44-3.5410.90.3435080.9540.1050.361.43496.4
3.54-3.6510.40.2894880.9750.0890.3040.94895.5
3.65-3.788.50.2634690.9510.0940.2811.5691.2
3.78-3.9490.2424830.9670.0840.2571.46492.5
3.94-4.119.80.1714890.9880.0550.180.99795.7
4.11-4.3311.10.1315020.9930.0390.1370.92595.4
4.33-4.610.80.1044980.9950.0320.1090.87894.9
4.6-4.9610.80.0995070.9950.030.1040.83795.3
4.96-5.4611.10.0895010.9960.0270.0930.73195.1
5.46-6.2410.50.0765150.9960.0240.080.62194.3
6.24-7.8610.30.0635160.9980.020.0660.54793.5
7.86-509.40.0465580.9990.0150.0480.5691.6

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6M0J

6m0j


Resolution: 2.89→43.39 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2729 497 5.24 %
Rwork0.241 8992 -
obs0.2427 9489 90.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.11 Å2 / Biso mean: 49.3254 Å2 / Biso min: 25.5 Å2
Refinement stepCycle: final / Resolution: 2.89→43.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3064 0 0 0 3064
Num. residues----396
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.89-3.180.3971890.32711974206381
3.18-3.640.28691540.27192257241194
3.64-4.590.24981480.22372283243194
4.59-43.390.25151060.21592478258494

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