8YMJ | pdb_00008ymj

Cryo-EM structure of Hepatitis B virus surface antigen subviral particle with D2 symmetry

• PDB DOI: https://doi.org/10.2210/pdb8YMJ/pdb
• EM Map EMD-39395: EMDB EMDataResource

• Classification: VIRUS LIKE PARTICLE
• Organism(s): Hepatitis B virus ayw/China/Tibet127/2002
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2024-03-09 Released: 2024-09-18 
• Deposition Author(s): Wang, T., Cao, L., Mu, A., Wang, Q., Rao, Z.H.
• Funding Organization(s): National Natural Science Foundation of China (NSFC), Ministry of Science and Technology (MoST, China), Chinese Academy of Sciences

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 6.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

Inherent symmetry and flexibility in hepatitis B virus subviral particles.

Wang, Q., Wang, T., Cao, L., Mu, A., Fu, S., Wang, P., Gao, Y., Ji, W., Liu, Z., Du, Z., Guddat, L.W., Zhang, W., Li, S., Li, X., Lou, Z., Wang, X., Hu, Z., Rao, Z.

(2024) Science 385: 1217-1224

• PubMed: 39264996 
• DOI: https://doi.org/10.1126/science.adp1453
• Primary Citation of Related Structures:  
  8YMJ, 8YMK


• PubMed Abstract: 
  

  Chronic hepatitis B virus (HBV) infection poses a major global health challenge with massive morbidity and mortality. Despite a preventive vaccine, current treatments provide limited virus clearance, necessitating lifelong commitment. The HBV surface antigen (HBsAg) is crucial for diagnosis and prognosis, yet its high-resolution structure and assembly on the virus envelope remain elusive. Utilizing extensive datasets and advanced cryo-electron microscopy analysis, we present structural insights into HBsAg at a near-atomic resolution of 3.7 angstroms. HBsAg homodimers assemble into subviral particles with D ₂ - and D ₄ -like quasisymmetry, elucidating the dense-packing rules and structural adaptability of HBsAg. These findings provide insights into how HBsAg assembles into higher-order filaments and interacts with the capsid to form virions.

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Organizational Affiliation: 
• Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
Shanghai Clinical Research and Trial Center, Shanghai, China.
National Facility for Protein Science, Shanghai Advanced Research Institute, Chinese Academy of Sciences (CAS), Shanghai, China.
Laboratory of Structural Biology, Tsinghua University, Beijing, China.
State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Response, College of Life Sciences, and State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China.
National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, CAS, Beijing, China.
University of Chinese Academy of Sciences, Beijing, China.
School of Chemistry and Molecular Biosciences, the University of Queensland, Brisbane, Australia.
National Institutes for Food and Drug Control, Beijing, China.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 80-mer - A80 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 2,032.64 kDa 
• Atom Count: 97,912 
• Modeled Residue Count: 18,080 
• Deposited Residue Count: 18,080 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform S of Large envelope protein	A, AA [auth a], AB [auth 1], AC [auth AQ], B, BA [auth b], BB [auth 2], BC [auth AR], C, CA [auth c], CB [auth 3], D, DA [auth d], DB [auth 4], E, EA [auth e], EB [auth 5], F, FA [auth f], FB [auth 6], G, GA [auth g], GB [auth 7], H, HA [auth h], HB [auth 8], I, IA [auth i], IB [auth 9], J, JA [auth j], JB [auth 0], K, KA [auth k], KB [auth AA], L, LA [auth l], LB [auth AB], M, MA [auth m], MB [auth AC], N, NA [auth n], NB [auth AD], O, OA [auth o], OB [auth AE], P, PA [auth p], PB [auth AF], Q, QA [auth q], QB [auth AG], R, RA [auth r], RB [auth AH], S, SA [auth s], SB [auth AI], T, TA [auth t], TB [auth AJ], U, UA [auth u], UB [auth AK], V, VA [auth v], VB [auth AL], W, WA [auth w], WB [auth AM], X, XA [auth x], XB [auth AN], Y, YA [auth y], YB [auth AO], Z, ZA [auth z], ZB [auth AP]	226	Hepatitis B virus ayw/China/Tibet127/2002	Mutation(s): 0
UniProt
Find proteins for Q913A6 (Hepatitis B virus genotype C subtype ayw (isolate China/Tibet127/2002)) Explore Q913A6  Go to UniProtKB:  Q913A6

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 6.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX	1.20.1_4487:

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-18 
Deposition Author(s): Wang, T., Cao, L., Mu, A., Wang, Q., Rao, Z.H.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81520108019
National Natural Science Foundation of China (NSFC)	China	813300237
National Natural Science Foundation of China (NSFC)	China	31971118
Ministry of Science and Technology (MoST, China)	China	2017YFC0840300
Ministry of Science and Technology (MoST, China)	China	2020YFA0707500
Chinese Academy of Sciences	China	XDB08020200
Chinese Academy of Sciences	China	XDB37020203

Revision History  

• Version 1.0: 2024-09-18
  Type: Initial release
  
• Version 1.1: 2024-09-25
  Changes: Data collection, Database references
• Version 1.2: 2024-10-09
  Changes: Data collection, Structure summary