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- PDB-9cpx: Crystal structure of SARS-CoV-2 receptor binding domain in comple... -

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Basic information

Entry
Database: PDB / ID: 9cpx
TitleCrystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies C03-0138 and CC12.3
Components
  • (C03-0138 Fab ...) x 2
  • CC12.3 Fab heavy chain
  • CC12.3 Fab light chain
  • Spike protein S1
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / COVID-19 / SARS-CoV-2 / Receptor binding domain / 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 / entry receptor-mediated virion attachment to host cell / membrane fusion / 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 speciesMus musculus (house mouse)
Homo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsFeng, Z. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-004923 United States
CitationJournal: J.Exp.Med. / Year: 2025
Title: In vivo antibody diversification targeting a conserved coronavirus epitope.
Authors: Nair, U. / Feng, Z. / Akauliya, M. / Esposito, A.G. / Crain, C.R. / Lamperti, E.D. / Prum, T. / Warner, J.E. / Madungwe, L. / Dale, G.A. / Boucau, J. / Gaiha, G.D. / Yuan, M. / Wilson, I.A. / Batista, F.D.
History
DepositionJul 18, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: C03-0138 Fab heavy chain
L: C03-0138 Fab light chain
C: CC12.3 Fab heavy chain
D: CC12.3 Fab light chain
A: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,1776
Polymers117,5905
Non-polymers5871
Water36020
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11600 Å2
ΔGint-53 kcal/mol
Surface area45540 Å2
Unit cell
Length a, b, c (Å)110.168, 110.168, 226.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Antibody , 4 types, 4 molecules HLCD

#1: Antibody C03-0138 Fab heavy chain


Mass: 23397.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody C03-0138 Fab light chain


Mass: 24366.107 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Antibody CC12.3 Fab 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: Homo sapiens (human)
#4: Antibody CC12.3 Fab light chain


Mass: 23344.883 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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Protein / Sugars / Non-polymers , 3 types, 22 molecules A

#5: Protein Spike protein S1


Mass: 23104.867 Da / Num. of mol.: 1 / Fragment: Receptor binding domain (UNP residues 333-530)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P0DTC2
#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-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.92 Å3/Da / Density % sol: 57.93 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium citrate / citric acid buffer, pH 3.33, 25% v/v PEG200, 9% w/v PEG6000

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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: Apr 18, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.69→50 Å / Num. obs: 39168 / % possible obs: 99.9 % / Redundancy: 26.3 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.02 / Rrim(I) all: 0.103 / Χ2: 1.021 / Net I/σ(I): 11.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.69-2.7428.21.15519120.8310.9530.221.1760.815100
2.74-2.7927.61.02419230.860.9620.1971.0430.813100
2.79-2.8427.60.8218890.9060.9750.1580.8350.852100
2.84-2.927.30.719430.9310.9820.1350.7130.861100
2.9-2.9627.30.59319140.9490.9870.1150.6040.92100
2.96-3.03270.49419430.9610.990.0960.5030.969100
3.03-3.1126.80.40919220.9730.9930.080.4171.006100
3.11-3.1926.50.32719240.9850.9960.0640.3331.058100
3.19-3.2826.10.26219190.9860.9960.0520.2671.146100
3.28-3.3925.50.21619580.990.9970.0430.2211.21299.9
3.39-3.5124.90.17419440.9930.9980.0350.1781.278100
3.51-3.6521.40.14519410.9930.9980.0320.1481.291100
3.65-3.8225.80.12819310.9960.9990.0250.1311.19399.9
3.82-4.0228.20.11519550.9970.9990.0220.1171.21199.8
4.02-4.2727.80.09919700.9980.9990.0190.1011.17899.9
4.27-4.627.20.08619640.99810.0170.0881.12999.6
4.6-5.0626.80.07719800.99910.0150.0791.03999.7
5.06-5.7926.10.0720110.99910.0140.0710.93100
5.79-7.2922.60.06220370.99810.0130.0640.834100
7.29-5025.10.05321880.99910.0110.0540.75799.7

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_5127: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→49.54 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2705 3557 5.11 %
Rwork0.2295 --
obs0.2316 38939 95.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→49.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8065 0 39 20 8124
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002
X-RAY DIFFRACTIONf_angle_d0.5
X-RAY DIFFRACTIONf_dihedral_angle_d13.9382955
X-RAY DIFFRACTIONf_chiral_restr0.0431263
X-RAY DIFFRACTIONf_plane_restr0.0041438
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.740.3487790.29651528X-RAY DIFFRACTION55
2.74-2.780.3789950.29941766X-RAY DIFFRACTION64
2.78-2.820.31831130.30252078X-RAY DIFFRACTION74
2.82-2.860.36361390.28672451X-RAY DIFFRACTION89
2.86-2.910.39351490.29982680X-RAY DIFFRACTION97
2.91-2.960.33761470.30182747X-RAY DIFFRACTION99
2.96-3.010.41761520.30032781X-RAY DIFFRACTION100
3.01-3.070.36021460.29992793X-RAY DIFFRACTION100
3.07-3.130.321500.29642782X-RAY DIFFRACTION100
3.13-3.20.32971470.29672734X-RAY DIFFRACTION100
3.2-3.270.38331450.26542802X-RAY DIFFRACTION100
3.27-3.360.30491460.25232792X-RAY DIFFRACTION100
3.36-3.450.23021520.24012782X-RAY DIFFRACTION100
3.45-3.550.26041470.23112805X-RAY DIFFRACTION100
3.55-3.660.27641490.22592751X-RAY DIFFRACTION100
3.66-3.790.24251550.22222773X-RAY DIFFRACTION100
3.79-3.950.23191460.21752763X-RAY DIFFRACTION100
3.95-4.130.25091520.20192780X-RAY DIFFRACTION100
4.13-4.340.22231530.1912771X-RAY DIFFRACTION100
4.34-4.610.2381420.18022775X-RAY DIFFRACTION100
4.62-4.970.22131550.18072772X-RAY DIFFRACTION100
4.97-5.470.21931430.19532790X-RAY DIFFRACTION100
5.47-6.260.26231480.21112763X-RAY DIFFRACTION100
6.26-7.880.23381520.22182795X-RAY DIFFRACTION100
7.89-49.540.2241550.18822766X-RAY DIFFRACTION100

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