9IYX | pdb_00009iyx

Structure of HBV surface antigen determined in recombinant spherical subviral particle

• PDB DOI: https://doi.org/10.2210/pdb9IYX/pdb
• EM Map EMD-61003: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): HBV genotype D3
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2024-07-31 Released: 2025-01-15 
• Deposition Author(s): Chen, L., He, X.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of small HBV surface antigen reveals mechanism of dimer formation.

He, X., Kang, Y., Tao, W., Xu, J., Liu, X., Chen, L.

(2025) Cell Discov 11: 6-6

• PubMed: 39805867 
• DOI: https://doi.org/10.1038/s41421-024-00768-8
• Primary Citation of Related Structures:  
  9IYX

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Organizational Affiliation: 
• State Key Laboratory of Membrane Biology, College of Future Technology, Institute of Molecular Medicine, Peking University, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Beijing, China.
Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
State Key Laboratory of Membrane Biology, College of Future Technology, Institute of Molecular Medicine, Peking University, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Beijing, China. [e-mail].
Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China. [e-mail].
Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China. [e-mail].
National Biomedical Imaging Center, Peking University, Beijing, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 50.99 kDa 
• Atom Count: 2,626 
• Modeled Residue Count: 351 
• Deposited Residue Count: 452 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Large envelope protein	A, B	226	HBV genotype D3	Mutation(s): 0
UniProt
Find proteins for V9P415 (Hepatitis B virus) Explore V9P415  Go to UniProtKB:  V9P415

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-01-15 
Deposition Author(s): Chen, L., He, X.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31821091

Revision History  

• Version 1.0: 2025-01-15
  Type: Initial release
  
• Version 1.1: 2025-07-09
  Changes: Data collection, Database references