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- PDB-8sir: Crystal structure of SARS-CoV-2 spike receptor-binding domain in ... -

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Basic information

Entry
Database: PDB / ID: 8sir
TitleCrystal structure of SARS-CoV-2 spike receptor-binding domain in complex with broadly neutralizing antibody CC25.54 Fab
Components
  • CC25.54 Fab heavy chain
  • CC25.54 Fab light chain
  • Spike protein S1
KeywordsIMMUNE SYSTEM / bnAb / SARS-CoV-2 / broadly neutralizing antibody / spike / RBD
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 / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / membrane fusion ...symbiont-mediated disruption of host tissue / Maturation of spike protein / 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 / membrane fusion / entry receptor-mediated virion attachment to host cell / 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 / 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 / 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 / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus spike glycoprotein S1, receptor binding / 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
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsLiu, H. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-004923 United States
Citation
Journal: Cell Rep / Year: 2025
Title: Broadly neutralizing antibodies targeting a conserved silent face of spike RBD resist extreme SARS-CoV-2 antigenic drift.
Authors: Song, G. / Yuan, M. / Liu, H. / Capozzola, T. / Lin, R.N. / Torres, J.L. / He, W.T. / Musharrafieh, R. / Dueker, K. / Zhou, P. / Callaghan, S. / Mishra, N. / Yong, P. / Anzanello, F. / ...Authors: Song, G. / Yuan, M. / Liu, H. / Capozzola, T. / Lin, R.N. / Torres, J.L. / He, W.T. / Musharrafieh, R. / Dueker, K. / Zhou, P. / Callaghan, S. / Mishra, N. / Yong, P. / Anzanello, F. / Avillion, G. / Vo, A.L. / Li, X. / Zhang, Y. / Makhdoomi, M. / Feng, Z. / Zhu, X. / Peng, L. / Nemazee, D. / Safonova, Y. / Briney, B. / Ward, A.B. / Burton, D.R. / Wilson, I.A. / Andrabi, R.
#1: Journal: Biorxiv / Year: 2023
Title: Broadly neutralizing antibodies targeting a conserved silent face of spike RBD resist extreme SARS-CoV-2 antigenic drift
Authors: Song, G. / Yuan, M. / Liu, H. / Capozzola, T. / Lin, R. / Torres, J. / He, W. / Musharrafieh, R. / Dueker, K. / Zhou, P. / Callaghan, S. / Mishra, N. / Yong, P. / Anzanello, F. / Avillion, G. ...Authors: Song, G. / Yuan, M. / Liu, H. / Capozzola, T. / Lin, R. / Torres, J. / He, W. / Musharrafieh, R. / Dueker, K. / Zhou, P. / Callaghan, S. / Mishra, N. / Yong, P. / Anzanello, F. / Avillion, G. / Vo, A. / Li, X. / Makhdoomi, M. / Feng, Z. / Zhu, X. / Peng, L. / Nemazee, D. / Safonova, Y. / Briney, B. / Ward, A. / Burton, D. / Wilson, I. / Andrabi, R.
History
DepositionApr 16, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Jul 30, 2025Group: Database references / Category: citation / citation_author

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spike protein S1
H: CC25.54 Fab heavy chain
L: CC25.54 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7044
Polymers72,4833
Non-polymers2211
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.867, 135.867, 87.134
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#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: Trichoplusia ni (cabbage looper) / References: UniProt: P0DTC2
#2: Antibody CC25.54 Fab heavy chain


Mass: 25803.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse)
#3: Antibody CC25.54 Fab light chain


Mass: 23574.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse)
#4: 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
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: 3.2 Å3/Da / Density % sol: 61.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 3350, 0.2 M potassium sodium tartrate, pH 7.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 14256 / % possible obs: 99.8 % / Redundancy: 11.5 % / CC1/2: 0.988 / CC star: 0.997 / Rmerge(I) obs: 0.298 / Rpim(I) all: 0.091 / Rrim(I) all: 0.312 / Χ2: 0.913 / Net I/σ(I): 2.8 / Num. measured all: 164569
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
3.3-3.367.10.9787050.3210.6970.3811.0550.72998.7
3.36-3.4281.0626750.2870.6680.3881.1350.74599.4
3.42-3.489.10.9717170.8490.9580.3361.0310.82399.3
3.48-3.5510.11.0016880.6190.8740.3261.0550.80399.6
3.55-3.6310.80.987080.7060.910.3091.0290.81599.4
3.63-3.7211.40.996790.6740.8970.3061.0370.88799.9
3.72-3.8111.90.8577230.8030.9440.2570.8950.80899.9
3.81-3.9112.10.837010.8430.9560.2470.8670.885100
3.91-4.0312.50.6997080.8870.970.2050.7290.847100
4.03-4.1612.50.537100.9570.9890.1550.5530.868100
4.16-4.3112.50.4427030.9690.9920.1290.4610.914100
4.31-4.4812.40.367070.9690.9920.1060.3760.955100
4.48-4.6811.90.3117220.9830.9960.0940.3250.986100
4.68-4.93110.2577100.9760.9940.0810.271.005100
4.93-5.2413.60.2757180.9830.9960.0770.2860.965100
5.24-5.6413.50.2617130.9850.9960.0730.2720.961100
5.64-6.2113.40.2467300.9850.9960.0690.2551.01100
6.21-7.113.10.217230.9830.9960.060.2181.034100
7.1-8.9412.10.1267390.9950.9990.0370.1311.13100
8.94-5011.70.067770.99810.0180.0630.84299.9

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→48.76 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2356 542 4.85 %Random selection
Rwork0.2077 ---
obs0.2091 11186 78.48 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68 Å2
Refinement stepCycle: LAST / Resolution: 3.3→48.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4789 0 14 0 4803
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024927
X-RAY DIFFRACTIONf_angle_d0.5726732
X-RAY DIFFRACTIONf_dihedral_angle_d19.379690
X-RAY DIFFRACTIONf_chiral_restr0.045757
X-RAY DIFFRACTIONf_plane_restr0.005867
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.630.3401650.27561183X-RAY DIFFRACTION36
3.63-4.160.28181520.2462986X-RAY DIFFRACTION89
4.16-5.240.21591590.19213382X-RAY DIFFRACTION100
5.24-48.760.20491660.1883093X-RAY DIFFRACTION89
Refinement TLS params.Method: refined / Origin x: -47.16 Å / Origin y: 50.0553 Å / Origin z: 10.0501 Å
111213212223313233
T0.2632 Å2-0.1277 Å2-0.0094 Å2-0.626 Å20.1103 Å2--0.3717 Å2
L1.8534 °2-1.4002 °2-0.4906 °2-1.2027 °20.6427 °2--0.4559 °2
S0.0166 Å °-0.1812 Å °-0.0762 Å °0.0716 Å °0.0074 Å °0.1244 Å °0.0759 Å °-0.051 Å °-0.0108 Å °
Refinement TLS groupSelection details: all

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