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

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Basic information

Entry
Database: PDB / ID: 9cpr
TitleCrystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies M22-90 and CC12.3
Components
  • CC12.3 Fab heavy chain
  • CC12.3 Fab light chain
  • M22-90 Fab heavy chain
  • M22-90 Fab light chain
  • Spike protein S1
KeywordsViral Protein/IMMUNE SYSTEM / COVID-19 / SARS-CoV-2 / Receptor binding domain / Antibody / IMMUNE SYSTEM / 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
CITRIC ACID / Spike glycoprotein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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
A: Spike protein S1
F: CC12.3 Fab heavy chain
G: CC12.3 Fab light chain
H: M22-90 Fab heavy chain
L: M22-90 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,2437
Polymers117,6265
Non-polymers6172
Water362
1
A: Spike protein S1
F: CC12.3 Fab heavy chain
G: CC12.3 Fab light chain
hetero molecules

H: M22-90 Fab heavy chain
L: M22-90 Fab light chain


Theoretical massNumber of molelcules
Total (without water)118,2437
Polymers117,6265
Non-polymers6172
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_646-x+1,y-1/2,-z+11
Buried area10230 Å2
ΔGint-39 kcal/mol
Surface area46990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.366, 102.309, 136.478
Angle α, β, γ (deg.)90.00, 100.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Antibody , 4 types, 4 molecules FGHL

#2: 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)
#3: 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)
#4: Antibody M22-90 Fab heavy chain


Mass: 23451.428 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 M22-90 Fab light chain


Mass: 24347.965 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)

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Protein / Sugars , 2 types, 2 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 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-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
DGlcpNAcb1-6DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a6-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(6+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE

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Non-polymers , 2 types, 3 molecules

#7: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 3.23 Å3/Da / Density % sol: 61.94 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium citrate citric acid buffer (pH 4.33), 25% (v/v) polyethylene glycol 200, and 7% (w/v) 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: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 25404 / % possible obs: 91.6 % / Redundancy: 5.1 % / CC1/2: 0.932 / CC star: 0.982 / Rmerge(I) obs: 0.316 / Rpim(I) all: 0.147 / Rrim(I) all: 0.35 / Χ2: 0.9 / Net I/σ(I): 4.4 / Num. measured all: 130159
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
3.1-3.153.31.3510220.5130.8240.7031.5330.87473.3
3.15-3.213.61.04910670.5360.8360.5281.1830.81877.4
3.21-3.273.91.03210790.5530.8440.5091.1590.87479
3.27-3.3441.01111330.5840.8590.5031.1370.91682.9
3.34-3.414.30.87711770.6090.870.4260.9810.89585.4
3.41-3.494.50.69312210.7330.920.3310.7730.91588.2
3.49-3.584.60.70212280.720.9150.3410.7850.93289.8
3.58-3.684.80.58212980.760.9290.2790.650.89592.6
3.68-3.784.80.54512710.80.9430.2610.6080.92193.5
3.78-3.914.80.50513230.8070.9450.2460.5650.89194.8
3.91-4.0450.4212770.8620.9620.20.4680.96993.5
4.04-4.214.60.32612990.90.9730.1650.3680.94193.3
4.21-4.44.90.28812980.9280.9810.140.3221.03895.2
4.4-4.635.70.22314120.9580.9890.1010.2460.99299.2
4.63-4.925.80.2313720.9570.9890.1030.2530.99399.8
4.92-5.36.20.23713730.9560.9890.1030.2590.9599.5
5.3-5.836.50.27713850.950.9870.1180.3020.88999.4
5.83-6.676.60.30413850.9540.9880.1280.3310.83399.5
6.67-8.46.20.1913520.9730.9930.0820.2070.895.8
8.4-506.60.08714320.9870.9970.0360.0940.72198.9

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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: 3.1→48.07 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2472 1992 8.9 %
Rwork0.1942 --
obs0.1991 22381 80.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→48.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8074 0 41 2 8117
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002
X-RAY DIFFRACTIONf_angle_d0.487
X-RAY DIFFRACTIONf_dihedral_angle_d10.6872961
X-RAY DIFFRACTIONf_chiral_restr0.0421261
X-RAY DIFFRACTIONf_plane_restr0.0041447
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.170.3214900.2719885X-RAY DIFFRACTION50
3.17-3.250.3458980.26461067X-RAY DIFFRACTION58
3.25-3.350.34611120.2741082X-RAY DIFFRACTION62
3.35-3.450.34431090.24831226X-RAY DIFFRACTION68
3.45-3.580.28241250.21571259X-RAY DIFFRACTION71
3.58-3.720.27671330.22891370X-RAY DIFFRACTION76
3.72-3.890.28291430.21721421X-RAY DIFFRACTION80
3.89-4.10.2651500.21841525X-RAY DIFFRACTION86
4.1-4.350.27841550.191605X-RAY DIFFRACTION89
4.35-4.690.20811690.16811793X-RAY DIFFRACTION98
4.69-5.160.20991800.16371783X-RAY DIFFRACTION99
5.16-5.90.23481700.17771782X-RAY DIFFRACTION99
5.9-7.430.2551840.19841798X-RAY DIFFRACTION99
7.44-48.070.19521740.16591793X-RAY DIFFRACTION96

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