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- PDB-7det: Crystal structure of SARS-CoV-2 RBD in complex with a neutralizin... -

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Basic information

Entry
Database: PDB / ID: 7det
TitleCrystal structure of SARS-CoV-2 RBD in complex with a neutralizing antibody scFv
Components
  • Spike protein S1
  • antibody scFv
KeywordsVIRAL PROTEIN/ANTIVIRAL PROTEIN / SARS-CoV-2 / RBD / antibody / VIRAL PROTEIN / ANTIVIRAL PROTEIN / VIRAL PROTEIN-ANTIVIRAL PROTEIN complex
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 / viral translation / host extracellular space / 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 / viral translation / host extracellular space / 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
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWang, Y. / Zhang, G. / Li, X. / Rao, Z. / Guo, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31670731 China
National Natural Science Foundation of China (NSFC)31870733 China
CitationJournal: Plos Biol. / Year: 2021
Title: Structural basis for SARS-CoV-2 neutralizing antibodies with novel binding epitopes.
Authors: Fu, D. / Zhang, G. / Wang, Y. / Zhang, Z. / Hu, H. / Shen, S. / Wu, J. / Li, B. / Li, X. / Fang, Y. / Liu, J. / Wang, Q. / Zhou, Y. / Wang, W. / Li, Y. / Lu, Z. / Wang, X. / Nie, C. / Tian, ...Authors: Fu, D. / Zhang, G. / Wang, Y. / Zhang, Z. / Hu, H. / Shen, S. / Wu, J. / Li, B. / Li, X. / Fang, Y. / Liu, J. / Wang, Q. / Zhou, Y. / Wang, W. / Li, Y. / Lu, Z. / Wang, X. / Nie, C. / Tian, Y. / Chen, D. / Wang, Y. / Zhou, X. / Wang, Q. / Yu, F. / Zhang, C. / Deng, C. / Zhou, L. / Guan, G. / Shao, N. / Lou, Z. / Deng, F. / Zhang, H. / Chen, X. / Wang, M. / Liu, L. / Rao, Z. / Guo, Y.
History
DepositionNov 5, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1May 26, 2021Group: Database references / Category: citation / citation_author
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
Revision 1.2Nov 29, 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 1.3Nov 20, 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

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Assembly

Deposited unit
A: Spike protein S1
B: antibody scFv
C: Spike protein S1
D: antibody scFv
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,6266
Polymers107,1834
Non-polymers4422
Water5,621312
1
A: Spike protein S1
B: antibody scFv
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8133
Polymers53,5922
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Spike protein S1
D: antibody scFv
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8133
Polymers53,5922
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.970, 42.254, 104.414
Angle α, β, γ (deg.)90.000, 104.570, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Spike protein S1


Mass: 23159.947 Da / Num. of mol.: 2 / Fragment: RBD
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 scFv


Mass: 30431.764 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: 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: obtained synthetically / 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 1.91 Å3/Da / Density % sol: 35.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.2M sodium chloride, 0.1M Tris pH 8.5, 29% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 41108 / % possible obs: 99.1 % / Redundancy: 10.1 % / CC1/2: 0.994 / Rmerge(I) obs: 0.112 / Net I/σ(I): 18.6
Reflection shellResolution: 2.2→2.24 Å / Rmerge(I) obs: 0.514 / Mean I/σ(I) obs: 1.74 / Num. unique obs: 1853 / CC1/2: 0.815

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Processing

Software
NameVersionClassification
PHENIX1.14_3228refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CJF

7cjf


Resolution: 2.2→46.472 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 27.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2599 1993 5.11 %
Rwork0.212 37007 -
obs0.2144 39000 94.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.11 Å2 / Biso mean: 34.9729 Å2 / Biso min: 12.53 Å2
Refinement stepCycle: final / Resolution: 2.2→46.472 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6658 0 28 312 6998
Biso mean--58.19 33.82 -
Num. residues----849
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2001-2.25510.3392860.2904158557
2.2551-2.31610.31621080.2623200872
2.3161-2.38420.30851350.2533250191
2.3842-2.46120.31781500.2352793100
2.4612-2.54910.31741500.23672787100
2.5491-2.65120.29811510.24432789100
2.6512-2.77190.32031490.23822779100
2.7719-2.9180.29191500.22962782100
2.918-3.10080.27681520.22782798100
3.1008-3.34010.22981510.22052817100
3.3401-3.67610.24431500.19742798100
3.6761-4.20770.22861550.18232857100
4.2077-5.30010.20271530.17352844100
5.3001-46.4720.25741530.2101286997

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