9KQR | pdb_00009kqr

Cryo-EM Structure of Mature Semliki Forest Virus

• PDB DOI: https://doi.org/10.2210/pdb9KQR/pdb
• EM Map EMD-62513: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Semliki Forest virus
• Mutation(s): No 
• Membrane Protein: Yes  MemProtMD


• Deposited: 2024-11-26 Released: 2025-10-22 
• Deposition Author(s): Jia, X., Li, S., Zhang, Q., He, J.
• Funding Organization(s): Other government

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.73 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural study of Semliki Forest virus through Cryo-EM

Jia, X., Li, S., Yu, H., Zhang, Q., He, J.

(2025) Dian Zi Xian Wei Xue Bao 44: 1

• DOI: https://doi.org/10.3969/j.issn.1000-6281.2025.01.03

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 12-mer - A4B4C4 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - C2 Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 497.12 kDa 
• Atom Count: 31,424 
• Modeled Residue Count: 4,084 
• Deposited Residue Count: 4,508 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein E2	A [auth k], D [auth b], G [auth e], J [auth h]	422	Semliki Forest virus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P0DJZ6 (Semliki forest virus) Explore P0DJZ6  Go to UniProtKB:  P0DJZ6

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein	B [auth l], E [auth c], H [auth f], K [auth i]	267	Semliki Forest virus	Mutation(s): 0  EC: 3.4.21.90 Membrane Entity: Yes
UniProt
Find proteins for P0DJZ6 (Semliki forest virus) Explore P0DJZ6  Go to UniProtKB:  P0DJZ6

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein E1	C [auth j], F [auth a], I [auth d], L [auth g]	438	Semliki Forest virus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P03315 (Semliki forest virus) Explore P03315  Go to UniProtKB:  P03315

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.73 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-10-22 
Deposition Author(s): Jia, X., Li, S., Zhang, Q., He, J.

---

Funding Organization	Location	Grant Number
Other government	China	2021B1212040017

Revision History  

• Version 1.0: 2025-10-22
  Type: Initial release