8X0L

Cryo-EM structure of Semliki Forest virus in complex with its receptor VLDLR(3-fold)

• PDB DOI: https://doi.org/10.2210/pdb8X0L/pdb
• EM Map EMD-37981: EMDB EMDataResource

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


• Deposited: 2023-11-04 Released: 2024-11-27 
• Deposition Author(s): Gao, F.G., Liu, S.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of Semliki Forest virus in complex with its receptor VLDLR(2-fold)

Gao, F.G., Liu, S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 12-mer - A3B3C3D3 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 350.95 kDa 
• Atom Count: 24,555 
• Modelled Residue Count: 3,165 
• Deposited Residue Count: 3,165 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein	A, D [auth E], G [auth I]	162	Semliki Forest virus	Mutation(s): 0
UniProt
Find proteins for P03315 (Semliki forest virus) Explore P03315  Go to UniProtKB:  P03315

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
pike glycoprotein E2	B, E [auth F], H [auth J]	418	Semliki Forest virus	Mutation(s): 0
Glycosylation
Glycosylation Sites: 2

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
pike glycoprotein E1	C, F [auth G], I [auth K]	438	Semliki Forest virus	Mutation(s): 0
UniProt
Find proteins for A0A0F6PP03 (Semliki forest virus) Explore A0A0F6PP03  Go to UniProtKB:  A0A0F6PP03
Glycosylation
Glycosylation Sites: 1

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Very low-density lipoprotein receptor	J [auth H], K [auth D], L	37	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: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	M, N, O, P, Q, R	2		N-Glycosylation

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	S [auth C], T [auth G], U [auth K]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA (Subject of Investigation/LOI)	V [auth H], W [auth D], X [auth L]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-11-27 
Deposition Author(s): Gao, F.G., Liu, S.

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

Revision History  

• Version 1.0: 2024-11-27
  Type: Initial release