9XI8 | pdb_00009xi8

Sarbecovirus GX2013 Spike S1 in complex with C092 Fab

• PDB DOI: https://doi.org/10.2210/pdb9XI8/pdb
• EM Map EMD-66900: EMDB EMDataResource

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Homo sapiens, BtRs-BetaCoV/GX2013
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2025-11-02 Released: 2026-08-12 
• Deposition Author(s): Niu, C., Liu, B., Gao, X., Li, Z., He, J., Xiong, X.
• Funding Organization(s): Other government, National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.45 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

AI identifies Elite Antibodies that Tolerate Escape Mutations from a Population Antibody Class Exerting Continued Selection Over SARS-CoV-2

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.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 186.12 kDa 
• Atom Count: 4,622 
• Modeled Residue Count: 612 
• Deposited Residue Count: 1,701 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of C092 Fab	A [auth H]	228	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of C092 Fab	B [auth L]	217	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	C [auth A]	1,256	BtRs-BetaCoV/GX2013	Mutation(s): 0
UniProt
Find proteins for A0A0U1WHJ8 (BtRs-BetaCoV/GX2013) Explore A0A0U1WHJ8  Go to UniProtKB:  A0A0U1WHJ8

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.45 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.19.1_4122
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-08-12 
Deposition Author(s): Niu, C., Liu, B., Gao, X., Li, Z., He, J., Xiong, X.

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Funding Organization	Location	Grant Number
Other government		2021YFA1300903
National Natural Science Foundation of China (NSFC)	China	82341085
Other government		EKPG21-06
Other government		SRPG22-002
Other government		2021A1515011289
Other government		2023B1212060050
Other government		2023B1212120009
Other government		GIBHBRP24-02

Revision History  

• Version 1.0: 2026-08-12
  Type: Initial release