8YVZ | pdb_00008yvz

Semliki Forest virus viron

• PDB DOI: https://doi.org/10.2210/pdb8YVZ/pdb
• EM Map EMD-39617: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Semliki Forest virus 4, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2024-03-29 Released: 2024-12-11 
• Deposition Author(s): Wang, J., Zheng, T., Yang, D.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

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

Literature

Structure of Semliki Forest virus at 3.02 Angstroms resolution

Zheng, T.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 20-mer - A4B4C4D4E4 

Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Homo 3-mer - B3 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 496.83 kDa 
• Atom Count: 34,740 
• Modeled Residue Count: 4,452 
• Deposited Residue Count: 4,452 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein E1	A, E [auth F], F [auth G], G [auth H]	438	Semliki Forest virus 4	Mutation(s): 0
UniProt
Find proteins for P03315 (Semliki forest virus) Explore P03315  Go to UniProtKB:  P03315
Glycosylation
Glycosylation Sites: 1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein E2	B, H [auth I], I [auth J], J [auth K]	418	Semliki Forest virus 4	Mutation(s): 0
UniProt
Find proteins for P03315 (Semliki forest virus) Explore P03315  Go to UniProtKB:  P03315
Glycosylation
Glycosylation Sites: 2

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein E3	C, K [auth L], L [auth M], M [auth N]	52	Semliki Forest virus 4	Mutation(s): 0
UniProt
Find proteins for P03315 (Semliki forest virus) Explore P03315  Go to UniProtKB:  P03315

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
capsid protein, partial	D, N [auth O], O [auth P], P [auth Q]	161	Semliki Forest virus 4	Mutation(s): 0
UniProt
Find proteins for P03315 (Semliki forest virus) Explore P03315  Go to UniProtKB:  P03315

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Very low-density lipoprotein receptor	Q [auth E], R, S, T	44	Homo sapiens	Mutation(s): 0  Gene Names: VLDLR
UniProt & NIH Common Fund Data Resources
Find proteins for P98155 (Homo sapiens) Explore P98155  Go to UniProtKB:  P98155
PHAROS:  P98155 GTEx:  ENSG00000147852

Oligosaccharides

Help

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth a], BA [auth b], CA [auth c], DA [auth d], EA [auth e], FA [auth f], U, V, W, X, Y, Z	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	GA [auth E], HA [auth R], IA [auth S], JA [auth T]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-12-11 
Deposition Author(s): Wang, J., Zheng, T., Yang, D.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-12-11
  Type: Initial release
  
• Version 1.1: 2025-07-23
  Changes: Data collection