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- PDB-9xi8: Sarbecovirus GX2013 Spike S1 in complex with C092 Fab -

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Basic information

Entry
Database: PDB / ID: 9xi8
TitleSarbecovirus GX2013 Spike S1 in complex with C092 Fab
Components
  • Heavy chain of C092 Fab
  • Light chain of C092 Fab
  • Spike glycoprotein
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Spike protein / Antibody Fab fragment / Complex / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


positive regulation of viral entry into host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / host cell surface receptor binding / 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 / host cell plasma membrane / virion membrane ...positive regulation of viral entry into host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / host cell surface receptor binding / 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 / host cell plasma membrane / virion membrane / membrane / identical protein binding
Similarity search - Function
Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / 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 (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / 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
Biological speciesHomo sapiens (human)
BtRs-BetaCoV/GX2013 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.45 Å
AuthorsNiu, C. / Liu, B. / Gao, X. / Li, Z. / He, J. / Xiong, X.
Funding support China, 8items
OrganizationGrant numberCountry
Other government2021YFA1300903
National Natural Science Foundation of China (NSFC)82341085 China
Other governmentEKPG21-06
Other governmentSRPG22-002
Other government2021A1515011289
Other government2023B1212060050
Other government2023B1212120009
Other governmentGIBHBRP24-02
CitationJournal: To Be Published
Title: AI identifies Elite Antibodies that Tolerate Escape Mutations from a Population Antibody Class Exerting Continued Selection Over SARS-CoV-2
Authors: Niu, C. / Huang, X. / Yan, Q. / Liu, B. / Gao, X. / Song, Y. / Wang, J. / Wang, L. / Li, Z. / Zheng, H. / He, P. / Huang, X. / Yuan, H. / Zou, B. / Yang, Y. / Wu, F. / Yao, Y. / Chen, X. / ...Authors: Niu, C. / Huang, X. / Yan, Q. / Liu, B. / Gao, X. / Song, Y. / Wang, J. / Wang, L. / Li, Z. / Zheng, H. / He, P. / Huang, X. / Yuan, H. / Zou, B. / Yang, Y. / Wu, F. / Yao, Y. / Chen, X. / Chen, L. / He, J. / Yao, J. / Zhao, J. / Xiong, X.
History
DepositionNov 2, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 12, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Heavy chain of C092 Fab
L: Light chain of C092 Fab
A: Spike glycoprotein


Theoretical massNumber of molelcules
Total (without water)186,1183
Polymers186,1183
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Antibody Heavy chain of C092 Fab


Mass: 24114.055 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Light chain of C092 Fab


Mass: 22886.127 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: Protein Spike glycoprotein / S glycoprotein / E2 / Peplomer protein


Mass: 139117.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BtRs-BetaCoV/GX2013 (virus) / Production host: Homo sapiens (human) / References: UniProt: A0A0U1WHJ8
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Sarbecovirus GX2013 Spike S1 in complex with C092 Fab / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Source (natural)Organism: BtRs-BetaCoV/GX2013 (virus)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
9PHENIX1.19.1_4122model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 385893 / Symmetry type: POINT
RefinementHighest resolution: 3.45 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0034740
ELECTRON MICROSCOPYf_angle_d0.6036472
ELECTRON MICROSCOPYf_dihedral_angle_d4.099666
ELECTRON MICROSCOPYf_chiral_restr0.044734
ELECTRON MICROSCOPYf_plane_restr0.004830

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