9XI6 | pdb_00009xi6

SARS-CoV-2 Omicron BA.4/5 spike RBD in complex with BD56-597 Fab and ACE2

• PDB DOI: https://doi.org/10.2210/pdb9XI6/pdb
• EM Map EMD-66898: EMDB EMDataResource

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM/HYDROLASE
• Organism(s): Homo sapiens, Severe acute respiratory syndrome coronavirus 2
• Expression System: Homo sapiens
• Mutation(s): Yes 


• 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: 2.60 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 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 139.63 kDa 
• Atom Count: 9,666 
• Modeled Residue Count: 1,224 
• Deposited Residue Count: 1,243 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Processed angiotensin-converting enzyme 2	A	602	Homo sapiens	Mutation(s): 0  Gene Names: ACE2, UNQ868/PRO1885 EC: 3.4.17 (UniProt), 3.4.17.23 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYF1 (Homo sapiens) Explore Q9BYF1  Go to UniProtKB:  Q9BYF1
PHAROS:  Q9BYF1 GTEx:  ENSG00000130234
Glycosylation
Glycosylation Sites: 4		Go to GlyGen: Q9BYF1-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	B [auth E]	196	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 17  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of BD56-597 Fab	C [auth H]	228	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of BD56-597 Fab	D [auth L]	217	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	F [auth A], G [auth A], H [auth A], I [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
ZN	E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.60 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