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- PDB-6xc7: Crystal structure of SARS-CoV-2 receptor binding domain in comple... -

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Basic information

Entry
Database: PDB / ID: 6xc7
TitleCrystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies CC12.3 and CR3022
Components
  • CC12.3 heavy chain
  • CC12.3 light chain
  • CR3022 heavy chain
  • CR3022 light chain
  • Spike protein S1
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / Antibody / SARS-CoV-2 / Coronavirus / Spike / IMMUNE SYSTEM / IMMUNE SYSTEM-VIRAL PROTEIN complex
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 / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / membrane / identical protein binding / 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 / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / 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 ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / 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 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.883 Å
AuthorsYuan, M. / Liu, H. / Wu, N.C. / Zhu, X. / Wilson, I.A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI139445 United States
Bill & Melinda Gates FoundationOPP1170236 United States
Consortia for HIV/AIDS Vaccine DevelopmentUM1 AI44462 United States
Citation
Journal: Science / Year: 2020
Title: Structural basis of a shared antibody response to SARS-CoV-2.
Authors: Yuan, M. / Liu, H. / Wu, N.C. / Lee, C.D. / Zhu, X. / Zhao, F. / Huang, D. / Yu, W. / Hua, Y. / Tien, H. / Rogers, T.F. / Landais, E. / Sok, D. / Jardine, J.G. / Burton, D.R. / Wilson, I.A.
#1: Journal: Biorxiv / Year: 2020
Title: Structural basis of a public antibody response to SARS-CoV-2.
Authors: Yuan, M. / Liu, H. / Wu, N.C. / Lee, C.D. / Zhu, X. / Zhao, F. / Huang, D. / Yu, W. / Hua, Y. / Tien, H. / Rogers, T.F. / Landais, E. / Sok, D. / Jardine, J.G. / Burton, D.R. / Wilson, I.A.
History
DepositionJun 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 16, 2020Group: Database references / Structure summary / Category: chem_comp / citation / citation_author / Item: _chem_comp.pdbx_synonyms
Revision 2.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spike protein S1
H: CR3022 heavy chain
L: CR3022 light chain
C: CC12.3 heavy chain
D: CC12.3 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,3236
Polymers120,7375
Non-polymers5871
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.873, 110.873, 228.490
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 2 types, 2 molecules AH

#1: Protein Spike protein S1


Mass: 26095.348 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: Trichoplusia ni (cabbage looper) / References: UniProt: P0DTC2
#2: Protein CR3022 heavy chain


Mass: 23455.420 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Antibody , 3 types, 3 molecules LCD

#3: Antibody CR3022 light chain


Mass: 24376.963 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody CC12.3 heavy chain


Mass: 23377.150 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse)
#5: Antibody CC12.3 light chain


Mass: 23431.963 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse)

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Sugars , 1 types, 1 molecules

#6: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE

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Details

Has ligand of interestN

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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: 2.91 Å3/Da / Density % sol: 57.7 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop
Details: 0.1M Tris pH 8 15% ethylene glycol 1M lithium chloride 10% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.88→50 Å / Num. obs: 32939 / % possible obs: 99.9 % / Redundancy: 13.6 % / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.036 / Rrim(I) all: 0.134 / Χ2: 0.748 / Net I/σ(I): 5.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.88-2.9712.61.61621700.6520.4671.6830.388100
2.97-3.0413.71.33721290.7840.3731.3880.39799.9
3.04-3.1214.10.97921390.8690.2691.0160.397100
3.12-3.2214.30.73521540.9210.2010.7630.418100
3.22-3.32140.57221630.9460.1580.5940.42899.9
3.32-3.4413.80.40221620.9730.1110.4170.453100
3.44-3.5813.40.29821730.9850.0840.310.504100
3.58-3.74120.20921700.9890.0620.2180.562100
3.74-3.9414.40.18221770.9940.0490.1890.611100
3.94-4.1814.80.13621900.9960.0360.1410.731100
4.18-4.514.20.10522030.9970.0290.1090.938100
4.5-4.9613.50.08521890.9980.0240.0891.10999.8
4.96-5.67120.07422380.9980.0220.0781.114100
5.67-7.1514.70.07322750.9980.0190.0751.203100
7.15-5012.40.04224070.9990.0120.0441.91199.1

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YLA, 4TSA, 4ZD3

6yla

4tsa

4zd3


Resolution: 2.883→42.25 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 25.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2591 1654 5.03 %
Rwork0.2189 31214 -
obs0.2209 32868 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 202.33 Å2 / Biso mean: 76.4035 Å2 / Biso min: 44.99 Å2
Refinement stepCycle: final / Resolution: 2.883→42.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8152 0 39 0 8191
Biso mean--91.94 --
Num. residues----1065
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8835-2.96830.35191420.3389247597
2.9683-3.06410.34291350.3192559100
3.0641-3.17350.38091340.28392577100
3.1735-3.30060.31991400.28222543100
3.3006-3.45070.3361310.26352571100
3.4507-3.63250.30261230.25012592100
3.6325-3.860.29051300.23192581100
3.86-4.15780.24711420.21132603100
4.1578-4.57580.25771460.17812597100
4.5758-5.23680.17631460.16682635100
5.2368-6.59380.2281410.20932666100
6.5938-42.250.24281440.2068281599

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