8UA8

Structure of Semliki Forest virus VLP in complex with VLDLR LA2

• PDB DOI: https://doi.org/10.2210/pdb8UA8/pdb
• EM Map EMD-42054: EMDB EMDataResource

• Classification: VIRUS LIKE PARTICLE
• Organism(s): Semliki Forest virus, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2023-09-20 Released: 2024-08-14 
• Deposition Author(s): Abraham, J., Yang, P., Li, W., Fan, X., Pan, J.
• Funding Organization(s): Burroughs Wellcome Fund

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of SFV VLP-VLDLRAD2 complex at the 3-fold axes

Abraham, J., Yang, P., Li, W., Fan, X., Pan, J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 17-mer - A4B4C4D4E1 

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: 476.84 kDa 
• Atom Count: 33,212 
• Modelled Residue Count: 4,267 
• Deposited Residue Count: 4,285 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoprotein E1	A, E, I, M	438	Semliki Forest virus	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
Glycoprotein E2	B, F, J, N	417	Semliki Forest virus	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
Assembly protein E3	C, G, K, O	54	Semliki Forest virus	Mutation(s): 0
UniProt
Find proteins for P03315 (Semliki forest virus) Explore P03315  Go to UniProtKB:  P03315
Glycosylation
Glycosylation Sites: 1

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein	D, H, L, P	153	Semliki Forest virus	Mutation(s): 0  EC: 3.4.21.90
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 R]	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: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth a], R [auth Q], U, V, W, X	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 7
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	BA [auth b], CA [auth c], S, T, Y, Z	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	DA [auth G], EA [auth K]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA (Subject of Investigation/LOI)	FA [auth R]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-08-14 
Deposition Author(s): Abraham, J., Yang, P., Li, W., Fan, X., Pan, J.

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Funding Organization	Location	Grant Number
Burroughs Wellcome Fund	United States	--

Revision History  

• Version 1.0: 2024-08-14
  Type: Initial release
  
• Version 1.1: 2024-10-23
  Changes: Data collection, Structure summary