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

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Basic information

Entry
Database: PDB / ID: 9cpu
TitleCrystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies C03-0304 and CC12.3
Components
  • (C03-0304 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 speciesSevere acute respiratory syndrome coronavirus 2
Mus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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
A: Spike protein S1
H: C03-0304 Fab heavy chain
F: CC12.3 Fab heavy chain
L: C03-0304 Fab light chain
G: CC12.3 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,2056
Polymers117,6185
Non-polymers5871
Water7,278404
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11000 Å2
ΔGint-50 kcal/mol
Surface area45800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.232, 110.232, 230.348
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11L-385-

HOH

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Components

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Antibody , 4 types, 4 molecules HFLG

#2: Antibody C03-0304 Fab heavy chain


Mass: 23487.443 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 C03-0304 Fab light chain


Mass: 24304.000 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)
#5: 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, 406 molecules A

#1: 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.: 404 / 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: 2.97 Å3/Da / Density % sol: 58.65 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris, pH 8, 15% v/v ethylene glycol, 1 M lithium chloride, 10% 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: 2.6→50 Å / Num. obs: 44734 / % possible obs: 99.9 % / Redundancy: 26.6 % / CC1/2: 0.97 / CC star: 0.992 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.02 / Rrim(I) all: 0.101 / Χ2: 0.871 / Net I/σ(I): 10.8 / Num. measured all: 1188872
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.6-2.6427.81.59421880.8530.960.3031.6230.819100
2.64-2.6927.41.31822100.8840.9690.2531.3420.96100
2.69-2.7428.41.07721770.9130.9770.2031.0970.834100
2.74-2.827.70.87221770.9340.9830.1670.8880.834100
2.8-2.8627.60.73322180.9520.9880.140.7460.847100
2.86-2.9327.50.5922010.9640.9910.1130.6010.863100
2.93-327.20.45622060.9740.9930.0880.4640.881100
3-3.0827.10.37322210.980.9950.0720.380.882100
3.08-3.1726.80.28122050.9830.9960.0550.2870.907100
3.17-3.2826.40.21921960.9860.9960.0430.2230.914100
3.28-3.3925.70.17322290.9880.9970.0340.1770.934100
3.39-3.5324.70.14522180.990.9980.030.1481.073100
3.53-3.6921.80.12122140.9830.9960.0270.1241.00699.1
3.69-3.8827.30.10422310.9940.9980.020.1060.93199.9
3.88-4.1328.10.09122570.9970.9990.0170.0930.925100
4.13-4.4527.90.07922450.9980.9990.0150.0810.838100
4.45-4.8927.20.07422590.99810.0140.0750.803100
4.89-5.626.60.07122950.9980.9990.0140.0730.764100
5.6-7.0523.80.06723010.9960.9990.0140.0690.71899.1
7.05-5024.90.06424860.990.9970.0130.0650.73199.4

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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: 2.6→49.3 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2389 2000 4.52 %
Rwork0.2061 --
obs0.2076 44210 98.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→49.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8078 0 39 404 8521
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002
X-RAY DIFFRACTIONf_angle_d0.478
X-RAY DIFFRACTIONf_dihedral_angle_d13.8182958
X-RAY DIFFRACTIONf_chiral_restr0.0421262
X-RAY DIFFRACTIONf_plane_restr0.0041445
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.660.32081250.25672628X-RAY DIFFRACTION88
2.66-2.730.33481380.27012915X-RAY DIFFRACTION98
2.73-2.810.30261410.25563003X-RAY DIFFRACTION100
2.81-2.90.31691440.2593018X-RAY DIFFRACTION100
2.9-3.010.27681420.24872999X-RAY DIFFRACTION100
3.01-3.130.32571420.23953003X-RAY DIFFRACTION100
3.13-3.270.25131420.23432997X-RAY DIFFRACTION100
3.27-3.440.26451440.22933042X-RAY DIFFRACTION100
3.44-3.660.21481440.20093019X-RAY DIFFRACTION99
3.66-3.940.22171440.19583037X-RAY DIFFRACTION100
3.94-4.340.20571440.17573054X-RAY DIFFRACTION100
4.34-4.960.1771470.16013093X-RAY DIFFRACTION100
4.96-6.250.20681480.1863127X-RAY DIFFRACTION100
6.25-49.30.22371550.18593275X-RAY DIFFRACTION99

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