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

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Basic information

Entry
Database: PDB / ID: 9cpv
TitleCrystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies C03-0614 and CC12.3
Components
  • (C03-0614 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


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 / 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 / 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
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: 3 Å
AuthorsFeng, Z. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-004923 United States
CitationJournal: To Be Published
Title: Structures of CR3022-like antibodies
Authors: Feng, Z. / Wilson, I.A.
History
DepositionJul 18, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: C03-0614 Fab heavy chain
L: C03-0614 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)118,1246
Polymers117,5375
Non-polymers5871
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11410 Å2
ΔGint-56 kcal/mol
Surface area45470 Å2
Unit cell
Length a, b, c (Å)110.538, 110.538, 224.937
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 C03-0614 Fab heavy chain


Mass: 23420.504 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 C03-0614 Fab light chain


Mass: 24289.885 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 , 2 types, 2 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

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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: 57.89 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium citrate / citric acid, pH 4.33, 25% v/v PEG200, 6% 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: 3→50 Å / Num. obs: 28903 / % possible obs: 99.9 % / Redundancy: 12.7 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.03 / Rrim(I) all: 0.109 / Χ2: 0.968 / Net I/σ(I): 10.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
3-3.0512.61.27414160.7430.9230.371.3280.825100
3.05-3.1112.61.05913940.7940.9410.3091.1040.832100
3.11-3.1712.40.86714350.8520.9590.2540.9040.855100
3.17-3.2312.40.70713920.8920.9710.2080.7370.87399.9
3.23-3.312.20.5814390.9150.9780.1720.6050.88599.9
3.3-3.38120.46314050.9380.9840.1380.4830.903100
3.38-3.4611.70.37114330.9540.9880.1120.3881.045100
3.46-3.5611.10.29414250.9730.9930.0920.3080.984100
3.56-3.669.70.23514090.9780.9940.0790.2481.031100
3.66-3.7811.80.21514130.9840.9960.0650.2251.023100
3.78-3.91130.18214620.990.9980.0520.191.068100
3.91-4.0713.30.14814190.9930.9980.0420.1531.083100
4.07-4.2613.40.11414530.9950.9990.0320.1181.084100
4.26-4.4813.80.09414370.9960.9990.0260.0971.166100
4.48-4.76140.07814360.9980.9990.0210.0811.14399.6
4.76-5.1314.40.07114500.9980.9990.0190.0731.06799.9
5.13-5.6414.30.06514730.9980.9990.0180.0680.98399.9
5.64-6.4613.60.0614810.9980.9990.0170.0630.91499.7
6.46-8.1312.30.04715080.99910.0140.0490.83999.9
8.13-5012.80.03516230.99910.010.0370.72699.3

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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: 3→49.6 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2617 2000 7.26 %
Rwork0.2074 --
obs0.2113 27562 95.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→49.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8069 0 39 0 8108
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002
X-RAY DIFFRACTIONf_angle_d0.523
X-RAY DIFFRACTIONf_dihedral_angle_d15.012953
X-RAY DIFFRACTIONf_chiral_restr0.0421260
X-RAY DIFFRACTIONf_plane_restr0.0041444
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.070.41171040.31941332X-RAY DIFFRACTION70
3.07-3.150.32751170.2821488X-RAY DIFFRACTION80
3.15-3.250.35771320.26791697X-RAY DIFFRACTION91
3.25-3.350.30491430.25951827X-RAY DIFFRACTION97
3.35-3.470.3331470.25421871X-RAY DIFFRACTION100
3.47-3.610.29151450.22271857X-RAY DIFFRACTION100
3.61-3.770.27041480.22411884X-RAY DIFFRACTION100
3.77-3.970.28811480.21141908X-RAY DIFFRACTION100
3.97-4.220.25571490.19251893X-RAY DIFFRACTION100
4.22-4.550.24421490.17311906X-RAY DIFFRACTION100
4.55-5.010.19051510.16561920X-RAY DIFFRACTION100
5.01-5.730.22981490.17921925X-RAY DIFFRACTION100
5.73-7.210.26521550.20921967X-RAY DIFFRACTION100
7.21-49.60.2071630.1822087X-RAY DIFFRACTION99

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