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

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Basic information

Entry
Database: PDB / ID: 9cps
TitleCrystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies M22-91 and CC12.3
Components
  • CC12.3 Fab heavy chain
  • CC12.3 Fab light chain
  • M22-91 Fab heavy chain
  • M22-91 Fab light chain
  • Spike protein S1
KeywordsIMMUNE SYSTEM/Viral Protein / COVID-19 / SARS-CoV-2 / Receptor binding domain / Antibody / IMMUNE SYSTEM / IMMUNE SYSTEM-Viral Protein 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
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: 3.03 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
F: CC12.3 Fab heavy chain
G: CC12.3 Fab light chain
H: M22-91 Fab heavy chain
L: M22-91 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,46914
Polymers117,5075
Non-polymers1,9619
Water00
1
F: CC12.3 Fab heavy chain
G: CC12.3 Fab light chain
hetero molecules

A: Spike protein S1
H: M22-91 Fab heavy chain
L: M22-91 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,46914
Polymers117,5075
Non-polymers1,9619
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_646-x+1,y-1/2,-z+11
Buried area12130 Å2
ΔGint-39 kcal/mol
Surface area47510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.637, 103.317, 135.531
Angle α, β, γ (deg.)90.00, 99.59, 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 M22-91 Fab heavy chain


Mass: 23407.355 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 M22-91 Fab light chain


Mass: 24272.939 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 / Non-polymers , 3 types, 10 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-(1-4)-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
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#7: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H8O7

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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: 3.27 Å3/Da / Density % sol: 62.37 %
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: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 3.02→50 Å / Num. obs: 29283 / % possible obs: 99.8 % / Redundancy: 6.8 % / CC1/2: 0.973 / CC star: 0.993 / Rmerge(I) obs: 0.276 / Rpim(I) all: 0.114 / Rrim(I) all: 0.299 / Χ2: 0.942 / Net I/σ(I): 3.3 / Num. measured all: 197924
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
3.02-3.076.51.30114500.4460.7860.5441.4120.84698.2
3.07-3.136.71.22314260.5470.8410.5061.3250.92999.5
3.13-3.196.81.12314470.6280.8790.4611.2150.9299.2
3.19-3.256.80.97114790.6460.8860.3971.050.97499.7
3.25-3.326.90.87514370.7640.9310.3550.9460.94899.8
3.32-3.470.72514370.810.9460.2930.7820.96299.8
3.4-3.4970.60814810.8410.9560.2480.6580.981100
3.49-3.5870.51514280.8910.9710.210.5571.031100
3.58-3.6970.45315050.8970.9730.1840.491.012100
3.69-3.86.90.39714290.9310.9820.1630.430.968100
3.8-3.946.80.3214930.950.9870.1320.3460.951100
3.94-4.16.60.26114390.9590.9890.110.2840.965100
4.1-4.286.10.19814840.9760.9940.0870.2170.947100
4.28-4.516.50.16514440.9840.9960.070.180.971100
4.51-4.7970.14714550.9860.9970.060.1590.95100
4.79-5.166.60.13614840.9880.9970.0570.1470.917100
5.16-5.686.50.13814730.9870.9970.0580.150.876100
5.68-6.57.40.14614860.9860.9970.0580.1570.909100
6.5-8.197.30.10914820.9920.9980.0430.1170.865100
8.19-5060.06315240.9960.9990.0280.0690.917100

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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: 3.03→48.02 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.253 1225 4.93 %
Rwork0.2148 --
obs0.2166 24857 84.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.03→48.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7898 0 132 0 8030
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001
X-RAY DIFFRACTIONf_angle_d0.433
X-RAY DIFFRACTIONf_dihedral_angle_d10.5992918
X-RAY DIFFRACTIONf_chiral_restr0.0411229
X-RAY DIFFRACTIONf_plane_restr0.0041425
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.03-3.150.38830.3011383X-RAY DIFFRACTION45
3.15-3.30.28261250.27762104X-RAY DIFFRACTION68
3.3-3.470.28761660.26782537X-RAY DIFFRACTION83
3.47-3.690.34541400.24832834X-RAY DIFFRACTION91
3.69-3.970.24921460.22532917X-RAY DIFFRACTION93
3.97-4.370.23261440.20222965X-RAY DIFFRACTION96
4.37-50.23931440.17973054X-RAY DIFFRACTION98
5-6.30.24921340.20122985X-RAY DIFFRACTION95
6.3-48.020.20841430.20312853X-RAY DIFFRACTION89

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