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

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Basic information

Entry
Database: PDB / ID: 8siq
TitleCrystal structure of SARS-CoV-2 spike receptor-binding domain in complex with broadly neutralizing antibodies CC25.36 and CV38-142 Fab
Components
  • (CV38-142 Fab ...) x 2
  • CC25.36 Fab heavy chain
  • CC25.36 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: 2.5 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 16, 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: CC25.36 Fab heavy chain
L: CC25.36 Fab light chain
M: CV38-142 Fab heavy chain
N: CV38-142 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,8816
Polymers118,1495
Non-polymers7331
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)60.399, 77.035, 266.445
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Antibody , 4 types, 4 molecules HLMN

#2: Antibody CC25.36 Fab heavy chain


Mass: 24429.301 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 CC25.36 Fab light chain


Mass: 22801.111 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: Antibody CV38-142 Fab heavy chain


Mass: 24068.002 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)
#5: Antibody CV38-142 Fab light chain


Mass: 23745.264 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)

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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: Trichoplusia ni (cabbage looper) / References: UniProt: P0DTC2
#6: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}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: 2.61 Å3/Da / Density % sol: 52.83 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop / Details: 20% (w/v) PEG-3350, 0.2 M di-Ammonium citrate

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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: Nov 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 38811 / % possible obs: 87.8 % / Redundancy: 3.5 % / CC1/2: 0.98 / CC star: 0.995 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.088 / Rrim(I) all: 0.181 / Χ2: 0.821 / Net I/σ(I): 5.8 / Num. measured all: 133906
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.5-2.543.31.11919700.5150.8240.661.3070.55392
2.54-2.593.31.08919820.4180.7680.6411.2720.55490.2
2.59-2.643.20.88519620.5310.8330.5271.0360.5891
2.64-2.693.20.80519100.5450.840.4690.9360.56489.1
2.69-2.753.10.65919820.70.9080.3950.7730.61989.3
2.75-2.823.10.62319090.6290.8790.3750.7310.64289.3
2.82-2.892.80.47819610.7020.9080.3040.570.67289.1
2.89-2.963.20.44519380.7320.9190.2610.5190.70588.5
2.96-3.053.40.40519130.8510.9590.2280.4680.74288
3.05-3.153.40.33418960.8850.9690.1860.3840.77186.9
3.15-3.263.30.27418660.8730.9650.1560.3170.83485.3
3.26-3.393.40.21719180.9320.9820.120.250.81787.1
3.39-3.553.40.17818790.9380.9840.0990.2051.03285.9
3.55-3.733.40.14719130.9360.9830.0810.1691.08286.8
3.73-3.973.30.11419310.9640.9910.0640.1321.06787.6
3.97-4.273.10.08519310.9750.9940.0490.0991.0986.2
4.27-4.73.90.06619280.9880.9970.0340.0751.07786.5
4.7-5.384.40.06219700.9880.9970.030.0690.95287.8
5.38-6.784.60.06620080.9890.9970.0310.0730.90387.3
6.78-504.10.03820440.9950.9990.020.0430.89183.8

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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: 2.5→38.52 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 31.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2871 1635 4.77 %
Rwork0.247 --
obs0.2489 34284 77.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→38.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7963 0 0 0 7963
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058162
X-RAY DIFFRACTIONf_angle_d0.76311134
X-RAY DIFFRACTIONf_dihedral_angle_d15.7081174
X-RAY DIFFRACTIONf_chiral_restr0.0451245
X-RAY DIFFRACTIONf_plane_restr0.0061433
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.570.4102680.40531312X-RAY DIFFRACTION38
2.57-2.660.4732880.35421831X-RAY DIFFRACTION53
2.66-2.750.39021040.32862409X-RAY DIFFRACTION69
2.75-2.860.39011450.30152690X-RAY DIFFRACTION78
2.86-2.990.35431430.29762966X-RAY DIFFRACTION86
2.99-3.150.35361390.30013018X-RAY DIFFRACTION87
3.15-3.350.30821380.28573008X-RAY DIFFRACTION86
3.35-3.60.29041610.25232999X-RAY DIFFRACTION87
3.6-3.970.30161660.22893029X-RAY DIFFRACTION87
3.97-4.540.20931580.19573041X-RAY DIFFRACTION86
4.54-5.720.21851520.19793139X-RAY DIFFRACTION88
5.72-38.520.2651730.22943207X-RAY DIFFRACTION86
Refinement TLS params.Method: refined / Origin x: -3.1396 Å / Origin y: -12.5512 Å / Origin z: 35.8211 Å
111213212223313233
T0.1493 Å2-0.0398 Å2-0.011 Å2-0.1452 Å20.0085 Å2--0.1757 Å2
L0.9276 °2-0.1415 °2-0.5146 °2-0.2381 °20.1801 °2--0.6039 °2
S-0.0644 Å °-0.0082 Å °-0.1423 Å °0.0957 Å °0.0287 Å °-0.0449 Å °0.0593 Å °0.0395 Å °0.0153 Å °
Refinement TLS groupSelection details: all

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