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- PDB-6xc3: Crystal structure of SARS-CoV-2 receptor binding domain in comple... -

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Basic information

Entry
Database: PDB / ID: 6xc3
TitleCrystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies CC12.1 and CR3022
Components
  • CC12.1 heavy chain
  • CC12.1 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 / 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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / Attachment and Entry / 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 speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.698 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 1.1Jul 15, 2020Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.pdbx_details
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 / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _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.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
Revision 2.3Nov 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

Downloads & links

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Assembly

Deposited unit
H: CR3022 heavy chain
L: CR3022 light chain
A: CC12.1 light chain
B: CC12.1 heavy chain
C: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,1446
Polymers120,7205
Non-polymers4241
Water3,063170
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.772, 109.772, 235.680
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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Antibody , 4 types, 4 molecules HLAB

#1: Antibody 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)
#2: 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)
#3: Antibody CC12.1 light chain


Mass: 23641.365 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)
#4: Antibody CC12.1 heavy chain


Mass: 23150.914 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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Protein / Sugars / Non-polymers , 3 types, 172 molecules C

#5: 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
#6: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.94 Å3/Da / Density % sol: 58.17 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 3000, 0.2 M sodium chloride, 0.1 M HEPES pH 7.5

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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: 2.698→50 Å / Num. obs: 40543 / % possible obs: 99.9 % / Redundancy: 10.7 % / Rmerge(I) obs: 0.167 / Rpim(I) all: 0.053 / Rrim(I) all: 0.175 / Χ2: 1.233 / Net I/σ(I): 5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.698-2.7671.05526550.6030.4161.1390.387100
2.76-2.838.40.90426440.7740.3250.9630.388100
2.83-2.91110.73426410.8660.230.770.41399.9
2.91-2.9911.90.5826620.9250.1750.6070.436100
2.99-3.09120.44726340.9520.1330.4670.48100
3.09-3.2120.35626690.9680.1060.3720.553100
3.2-3.3311.70.28226890.9760.0850.2950.66100
3.33-3.4811.40.22226650.9840.0680.2320.865100
3.48-3.6610.40.18326930.9860.0590.1921.083100
3.66-3.8910.90.16426840.9890.0510.1731.25499.9
3.89-4.1911.90.14427030.9920.0430.151.67100
4.19-4.6211.20.12127170.9940.0380.1262.3399.9
4.62-5.2810.40.11427420.9940.0370.122.483100
5.28-6.6510.70.10827800.9940.0340.1132.15199.9
6.65-5010.10.08329650.9960.0280.0882.97599.4

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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: 2.698→41.632 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2253 1963 4.85 %
Rwork0.1773 38499 -
obs0.1796 40462 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 169.16 Å2 / Biso mean: 49.4345 Å2 / Biso min: 19.71 Å2
Refinement stepCycle: final / Resolution: 2.698→41.632 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8136 0 28 170 8334
Biso mean--72.42 42.46 -
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 (%)
2.698-2.76550.34491450.2992266799
2.7655-2.84030.32311340.26022687100
2.8403-2.92380.29651250.23422717100
2.9238-3.01820.32121570.21812692100
3.0182-3.1260.32591310.21682726100
3.126-3.25110.2791410.21922709100
3.2511-3.3990.28441250.21642725100
3.399-3.57810.25121340.19872746100
3.5781-3.80220.22921460.18142731100
3.8022-4.09550.20651550.162736100
4.0955-4.50720.18071520.13542738100
4.5072-5.15840.16851360.12582794100
5.1584-6.4950.19651430.16042849100
6.495-41.6320.17851390.16298299

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