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- PDB-6xc2: Crystal structure of SARS-CoV-2 receptor binding domain in comple... -

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Basic information

Entry
Database: PDB / ID: 6xc2
TitleCrystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody CC12.1
Components
  • CC12.1 heavy chain
  • CC12.1 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: 3.112 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 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Sep 16, 2020Group: Database references / Structure summary / Category: chem_comp / citation / citation_author / Item: _chem_comp.pdbx_synonyms
Revision 1.3Oct 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

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Assembly

Deposited unit
A: Spike protein S1
L: CC12.1 light chain
H: CC12.1 heavy chain
Z: Spike protein S1
Y: CC12.1 light chain
X: CC12.1 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,2188
Polymers145,7756
Non-polymers4422
Water0
1
A: Spike protein S1
L: CC12.1 light chain
H: CC12.1 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,1094
Polymers72,8883
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
Z: Spike protein S1
Y: CC12.1 light chain
X: CC12.1 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,1094
Polymers72,8883
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.699, 143.494, 81.469
Angle α, β, γ (deg.)90.000, 118.680, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain Z
12chain H
22chain X
13chain L
23chain Y

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA334 - 1533
211chain ZZ334 - 1533
112chain HH1 - 216
212chain XX1 - 216
113chain LL1 - 215
213chain YY1 - 215

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Spike protein S1


Mass: 26095.348 Da / Num. of mol.: 2
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: Antibody CC12.1 light chain


Mass: 23641.365 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse)
#3: Antibody CC12.1 heavy chain


Mass: 23150.914 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse)
#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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
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: 2.84 Å3/Da / Density % sol: 56.67 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop
Details: 0.1M sodium citrate pH 5.5 15% polyethylene glycol 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.9795 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: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.11→50 Å / Num. obs: 25802 / % possible obs: 88.3 % / Redundancy: 1.5 % / CC1/2: 0.97 / Rmerge(I) obs: 0.16 / Net I/σ(I): 7.4
Reflection shellResolution: 3.2→3.27 Å / Num. unique obs: 1234 / CC1/2: 0.62

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Processing

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

4zd3

6yla


Resolution: 3.112→40.343 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 29.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2674 1289 5 %
Rwork0.2134 24488 -
obs0.2162 25777 88.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 140.13 Å2 / Biso mean: 70 Å2 / Biso min: 31.6 Å2
Refinement stepCycle: final / Resolution: 3.112→40.343 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9558 0 28 0 9586
Biso mean--97.74 --
Num. residues----1246
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1176X-RAY DIFFRACTION4.915TORSIONAL
12Z1176X-RAY DIFFRACTION4.915TORSIONAL
21H1278X-RAY DIFFRACTION4.915TORSIONAL
22X1278X-RAY DIFFRACTION4.915TORSIONAL
31L1292X-RAY DIFFRACTION4.915TORSIONAL
32Y1292X-RAY DIFFRACTION4.915TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.1122-3.23680.3532570.3031144347
3.2368-3.3840.33411500.2788287594
3.384-3.56240.30951250.2531299396
3.5624-3.78540.31732150.2297286296
3.7854-4.07740.27171540.2209291194
4.0774-4.48730.27811130.1796286892
4.4873-5.13550.17411190.1823275288
5.1355-6.46580.24581780.2075294997
6.4658-40.3430.26481780.2035283591

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