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- PDB-7x2h: Crystal structure of SARS-CoV-2 spike receptor-binding domain bou... -

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Basic information

Entry
Database: PDB / ID: 7x2h
TitleCrystal structure of SARS-CoV-2 spike receptor-binding domain bound with 6-2C Fab
Components
  • 6-2C H chain
  • 6-2C L chain
  • Spike protein S1
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 / antibody / VIRAL PROTEIN-IMMUNE SYSTEM 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 / 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: 2.1 Å
AuthorsWang, X. / Wang, Z.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2023
Title: Inactivated vaccine-elicited potent antibodies can broadly neutralize SARS-CoV-2 circulating variants.
Authors: Yubin Liu / Ziyi Wang / Xinyu Zhuang / Shengnan Zhang / Zhicheng Chen / Yan Zou / Jie Sheng / Tianpeng Li / Wanbo Tai / Jinfang Yu / Yanqun Wang / Zhaoyong Zhang / Yunfeng Chen / Liangqin ...Authors: Yubin Liu / Ziyi Wang / Xinyu Zhuang / Shengnan Zhang / Zhicheng Chen / Yan Zou / Jie Sheng / Tianpeng Li / Wanbo Tai / Jinfang Yu / Yanqun Wang / Zhaoyong Zhang / Yunfeng Chen / Liangqin Tong / Xi Yu / Linjuan Wu / Dong Chen / Renli Zhang / Ningyi Jin / Weijun Shen / Jincun Zhao / Mingyao Tian / Xinquan Wang / Gong Cheng /
Abstract: A full understanding of the inactivated COVID-19 vaccine-mediated antibody responses to SARS-CoV-2 circulating variants will inform vaccine effectiveness and vaccination development strategies. Here, ...A full understanding of the inactivated COVID-19 vaccine-mediated antibody responses to SARS-CoV-2 circulating variants will inform vaccine effectiveness and vaccination development strategies. Here, we offer insights into the inactivated vaccine-induced antibody responses after prime-boost vaccination at both the polyclonal and monoclonal levels. We characterized the VDJ sequence of 118 monoclonal antibodies (mAbs) and found that 20 neutralizing mAbs showed varied potency and breadth against a range of variants including XBB.1.5, BQ.1.1, and BN.1. Bispecific antibodies (bsAbs) based on nonoverlapping mAbs exhibited enhanced neutralizing potency and breadth against the most antibody-evasive strains, such as XBB.1.5, BQ.1.1, and BN.1. The passive transfer of mAbs or their bsAb effectively protected female hACE2 transgenic mice from challenge with an infectious Delta or Omicron BA.2 variant. The neutralization mechanisms of these antibodies were determined by structural characterization. Overall, a broad spectrum of potent and distinct neutralizing antibodies can be induced in individuals immunized with the SARS-CoV-2 inactivated vaccine BBIBP-CorV, suggesting the application potential of inactivated vaccines and these antibodies for preventing infection by SARS-CoV-2 circulating variants.
History
DepositionFeb 25, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2023Group: Data collection / Database references / Category: citation / citation_author / pdbx_validate_planes
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 / _pdbx_validate_planes.type
Revision 1.2Aug 23, 2023Group: Data collection
Category: chem_comp_atom / chem_comp_bond / pdbx_validate_planes
Item: _pdbx_validate_planes.type
Revision 1.3Oct 30, 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
A: 6-2C H chain
B: 6-2C L chain
C: 6-2C H chain
D: 6-2C L chain
E: Spike protein S1
F: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,1358
Polymers138,6936
Non-polymers4422
Water8,647480
1
A: 6-2C H chain
B: 6-2C L chain
E: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5684
Polymers69,3463
Non-polymers2211
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5910 Å2
ΔGint-31 kcal/mol
Surface area27020 Å2
MethodPISA
2
C: 6-2C H chain
D: 6-2C L chain
F: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5684
Polymers69,3463
Non-polymers2211
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5950 Å2
ΔGint-28 kcal/mol
Surface area27370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.053, 71.996, 112.761
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Antibody 6-2C H chain


Mass: 23999.707 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 6-2C L chain


Mass: 23445.145 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: Protein Spike protein S1


Mass: 21901.570 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: Trichoplusia ni (cabbage looper) / References: UniProt: P0DTC2
#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 / Feature type: SUBJECT OF INVESTIGATION
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.: 480 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.62 Å3/Da / Density % sol: 53.06 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.1M BIS-TRIS pH 6.5, 16% w/v Polyethylene glycol 10000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Dec 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 162158 / % possible obs: 99.8 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.989 / Χ2: 0.089 / Net I/σ(I): 5.7 / Num. measured all: 1092148
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.1-2.155.82.081108090.871100
2.15-2.26.31.897108060.8841100
2.2-2.264.61.128106902.014198.3
2.26-2.336.51.671108000.9011100
2.33-2.46.61.108108380.911100
2.4-2.497.40.917108270.9141100
2.49-2.597.40.775107990.9471100
2.59-2.717.40.548108480.9691100
2.71-2.857.30.405108511.0291100
2.85-3.037.30.269108111.0761100
3.03-3.267.10.183108471.1071100
3.26-3.596.90.119108241.0231100
3.59-4.116.10.094107601.039199.5
4.11-5.186.80.061108460.8281100
5.18-507.60.053108020.852199.5

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Processing

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

6m0j


Resolution: 2.1→31.52 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2689 4091 4.83 %
Rwork0.2283 --
obs0.2302 84635 99.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→31.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9513 0 28 480 10021
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099896
X-RAY DIFFRACTIONf_angle_d1.25913470
X-RAY DIFFRACTIONf_dihedral_angle_d14.3691369
X-RAY DIFFRACTIONf_chiral_restr0.0721479
X-RAY DIFFRACTIONf_plane_restr0.0121734
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.130.31711080.26522268X-RAY DIFFRACTION81
2.13-2.150.281410.2712729X-RAY DIFFRACTION100
2.15-2.180.2991340.27142776X-RAY DIFFRACTION100
2.18-2.210.3441390.28832776X-RAY DIFFRACTION100
2.21-2.240.42011440.40062666X-RAY DIFFRACTION98
2.24-2.270.46431450.45462736X-RAY DIFFRACTION99
2.27-2.310.39741420.322790X-RAY DIFFRACTION100
2.31-2.340.33191190.27132766X-RAY DIFFRACTION100
2.34-2.380.30371470.26192766X-RAY DIFFRACTION100
2.38-2.420.2741440.25652753X-RAY DIFFRACTION100
2.42-2.470.32511400.25982801X-RAY DIFFRACTION100
2.47-2.510.30261370.25492783X-RAY DIFFRACTION100
2.51-2.570.28091420.26042778X-RAY DIFFRACTION100
2.57-2.620.3441550.24592745X-RAY DIFFRACTION100
2.62-2.680.30211340.24152798X-RAY DIFFRACTION100
2.68-2.750.27251500.24082786X-RAY DIFFRACTION100
2.75-2.820.28971410.23642775X-RAY DIFFRACTION100
2.82-2.910.26561370.24272809X-RAY DIFFRACTION100
2.91-30.31051390.24862792X-RAY DIFFRACTION100
3-3.110.30461250.23992812X-RAY DIFFRACTION100
3.11-3.230.30761180.23582803X-RAY DIFFRACTION100
3.23-3.380.2431610.22332785X-RAY DIFFRACTION100
3.38-3.560.2551510.21322806X-RAY DIFFRACTION100
3.56-3.780.29491450.21392816X-RAY DIFFRACTION100
3.78-4.070.24221430.2032846X-RAY DIFFRACTION100
4.07-4.480.18611430.17132844X-RAY DIFFRACTION100
4.48-5.120.18941520.16842850X-RAY DIFFRACTION100
5.12-6.440.28841400.20132886X-RAY DIFFRACTION100
6.45-31.520.20311750.19193003X-RAY DIFFRACTION100

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