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

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Basic information

Entry
Database: PDB / ID: 9psp
TitleCrystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies BoWLB-1173 and CC12.3
Components
  • (BoWLB-1173 Fab ...) x 2
  • CC12.3 Fab heavy chain
  • CC12.3 Fab light chain
  • Spike protein S1 receptor binding domain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / COVID-19 / SARS-CoV-2 / Receptor binding domain / Antibody / IMMUNE SYSTEM / IMMUNE SYSTEM-Viral Protein complex / 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 / Lectin pathway of complement activation / host extracellular region / 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 / Lectin pathway of complement activation / host extracellular region / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / positive regulation of viral entry into host cell / Initial triggering of complement / membrane fusion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / Attachment and Entry / entry receptor-mediated virion attachment to host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / endocytosis involved in viral entry into host cell / receptor ligand activity / 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 / host cell plasma membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / virion membrane / membrane / identical protein binding / 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. / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal ...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. / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / 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 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
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / 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: 2.81 Å
AuthorsFeng, Z. / Wilson, I.A.
Funding support United States, 2items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-004923 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI190286 United States
CitationJournal: Cell Rep / Year: 2026
Title: In vivo evolution of antibody CR3022 expands cross-neutralization of SARS-CoV-2 variants and informs pan-sarbecovirus immunity.
Authors: Fu, Y. / Feng, Z. / Erickson, S.A. / Halfmann, P.J. / Li, L. / Chervin, J.C. / Troxell, C.A. / Sun, J. / Yasuhara, A. / Changrob, S. / Huang, M. / Zheng, N.Y. / Yuan, M. / Kawaoka, Y. / ...Authors: Fu, Y. / Feng, Z. / Erickson, S.A. / Halfmann, P.J. / Li, L. / Chervin, J.C. / Troxell, C.A. / Sun, J. / Yasuhara, A. / Changrob, S. / Huang, M. / Zheng, N.Y. / Yuan, M. / Kawaoka, Y. / Wilson, I.A. / Wilson, P.C.
History
DepositionJul 25, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2026Provider: repository / Type: Initial release
Revision 1.1May 27, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _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
T: Spike protein S1 receptor binding domain
U: Spike protein S1 receptor binding domain
K: CC12.3 Fab heavy chain
W: CC12.3 Fab light chain
M: CC12.3 Fab heavy chain
N: CC12.3 Fab light chain
H: BoWLB-1173 Fab heavy chain
L: BoWLB-1173 Fab light chain
A: BoWLB-1173 Fab heavy chain
B: BoWLB-1173 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,95021
Polymers236,17310
Non-polymers1,77711
Water4,990277
1
T: Spike protein S1 receptor binding domain
K: CC12.3 Fab heavy chain
W: CC12.3 Fab light chain
H: BoWLB-1173 Fab heavy chain
L: BoWLB-1173 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,03312
Polymers118,0875
Non-polymers9467
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
U: Spike protein S1 receptor binding domain
M: CC12.3 Fab heavy chain
N: CC12.3 Fab light chain
A: BoWLB-1173 Fab heavy chain
B: BoWLB-1173 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,9189
Polymers118,0875
Non-polymers8314
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.195, 101.051, 127.826
Angle α, β, γ (deg.)92.25, 100.66, 90.09
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules TU

#1: Protein Spike protein S1 receptor binding domain


Mass: 23520.311 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2

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Antibody , 4 types, 8 molecules KMWNHALB

#2: Antibody CC12.3 Fab heavy chain


Mass: 23377.150 Da / Num. of mol.: 2
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: 23431.963 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody BoWLB-1173 Fab heavy chain


Mass: 23327.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#5: Antibody BoWLB-1173 Fab light chain


Mass: 24430.154 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)

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Sugars , 2 types, 2 molecules

#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 natural 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: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 286 molecules

#8: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#9: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#10: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#11: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / 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: 2.96 Å3/Da / Density % sol: 58.51 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium citrate citric acid buffer (pH 4.0), 25% (v/v) polyethylene glycol 200, and 5% (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 19, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.81→50 Å / Num. obs: 65320 / % possible obs: 98.7 % / Redundancy: 3.2 % / CC1/2: 0.944 / CC star: 0.986 / Rmerge(I) obs: 0.172 / Rpim(I) all: 0.113 / Rrim(I) all: 0.207 / Χ2: 0.854 / Net I/σ(I): 5 / Num. measured all: 207911
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.81-2.8630.58432190.520.8270.3940.7070.6697.9
2.86-2.9130.52933030.6190.8740.3540.6390.68898.1
2.91-2.973.10.532360.6260.8780.3330.6020.71398.1
2.97-3.033.10.46632210.6660.8940.3090.5620.73398.5
3.03-3.093.20.40833160.7360.9210.2660.4890.74298.5
3.09-3.163.20.36632270.80.9430.240.4390.77898.5
3.16-3.243.20.31532700.8240.950.2060.3780.8198.5
3.24-3.333.20.28332230.8720.9650.1870.3410.84398.7
3.33-3.433.20.24532720.8720.9650.1620.2950.91698.6
3.43-3.543.10.20732770.9140.9770.140.2510.95698.7
3.54-3.672.80.19332520.9140.9770.1340.2361.13298.3
3.67-3.8130.17332500.930.9820.1170.210.90798.3
3.81-3.993.40.16833050.9360.9830.1080.2011.05898.9
3.99-4.23.40.13832630.9580.9890.0880.1640.90199
4.2-4.463.10.10732460.9660.9910.0720.130.91798.6
4.46-4.830.09432630.970.9920.0630.1140.83498.6
4.8-5.293.60.132850.9770.9940.0620.1180.84899.4
5.29-6.053.70.10632950.9770.9940.0650.1250.73799.6
6.05-7.623.60.09833120.9760.9940.060.1150.66699.6
7.62-502.80.05132850.9850.9960.0360.0631.38399.5

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PDB_EXTRACTdata extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.81→47.96 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 25.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2473 3215 5.05 %
Rwork0.1948 --
obs0.1974 63634 92.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.81→47.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16204 0 117 277 16598
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00216708
X-RAY DIFFRACTIONf_angle_d0.50922693
X-RAY DIFFRACTIONf_dihedral_angle_d15.2726036
X-RAY DIFFRACTIONf_chiral_restr0.0422523
X-RAY DIFFRACTIONf_plane_restr0.0042892
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.81-2.820.3509350.2565645X-RAY DIFFRACTION23
2.82-2.860.32751250.27512225X-RAY DIFFRACTION79
2.86-2.910.38721270.27172635X-RAY DIFFRACTION91
2.91-2.960.34241240.27242610X-RAY DIFFRACTION93
2.96-3.010.37081300.25582646X-RAY DIFFRACTION94
3.01-3.070.28811350.2492743X-RAY DIFFRACTION95
3.07-3.130.32881410.24252652X-RAY DIFFRACTION95
3.13-3.20.30651380.23722755X-RAY DIFFRACTION96
3.2-3.270.28781530.24832739X-RAY DIFFRACTION96
3.27-3.360.30111350.23982693X-RAY DIFFRACTION97
3.36-3.450.31181450.22992792X-RAY DIFFRACTION97
3.45-3.550.26041520.20642698X-RAY DIFFRACTION97
3.55-3.660.241360.20262815X-RAY DIFFRACTION97
3.66-3.790.27051640.18862677X-RAY DIFFRACTION97
3.79-3.940.25751470.17852817X-RAY DIFFRACTION97
3.94-4.120.22481450.1732763X-RAY DIFFRACTION98
4.12-4.340.19651510.15782737X-RAY DIFFRACTION98
4.34-4.610.17651510.14312833X-RAY DIFFRACTION98
4.61-4.970.1941360.14462791X-RAY DIFFRACTION99
4.97-5.470.19991580.15662788X-RAY DIFFRACTION99
5.47-6.260.21521780.1792763X-RAY DIFFRACTION99
6.26-7.880.26491570.19432822X-RAY DIFFRACTION99
7.88-47.960.19711520.18582780X-RAY DIFFRACTION99

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