2YEW

Modeling Barmah Forest virus structural proteins

• PDB DOI:  https://doi.org/10.2210/pdb2YEW/pdb
• EM Map EMD-1886: EMDB EMDataResource

• Classification: VIRUS
• Organism(s): Barmah Forest virus
• Expression System: Mesocricetus auratus
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTM


• Deposited: 2011-03-31 Released: 2012-04-18 
• Deposition Author(s): Kostyuchenko, V.A., Jakana, J., Liu, X., Haddow, A.D., Aung, M., Weaver, S.C., Chiu, W., Lok, S.M.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 5.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

The Structure of Barmah Forest Virus as Revealed by Cryo-Electron Microscopy at a 6-Angstrom Resolution Has Detailed Transmembrane Protein Architecture and Interactions.

Kostyuchenko, V.A., Jakana, J., Liu, X., Haddow, A.D., Aung, M., Weaver, S.C., Chiu, W., Lok, S.

(2011) J Virol 85: 9327

• PubMed: 21752915 
• DOI: https://doi.org/10.1128/JVI.05015-11
• Primary Citation of Related Structures:  
  2YEW


• PubMed Abstract: 
  

Barmah Forest virus (BFV) is a mosquito-borne alphavirus that infects humans. A 6-Å-resolution cryo-electron microscopy three-dimensional structure of BFV exhibits a typical alphavirus organization, with RNA-containing nucleocapsid surrounded by a bilipid membrane anchored with the surface proteins E1 and E2. The map allows details of the transmembrane regions of E1 and E2 to be seen. The C-terminal end of the E2 transmembrane helix binds to the capsid protein. Following the E2 transmembrane helix, a short α-helical endodomain lies on the inner surface of the lipid envelope. The E2 endodomain interacts with E1 transmembrane helix from a neighboring E1-E2 trimeric spike, thereby acting as a spacer and a linker between spikes. In agreement with previous mutagenesis studies, the endodomain plays an important role in recruiting other E1-E2 spikes to the budding site during virus assembly. The E2 endodomain may thus serve as a target for antiviral drug design.

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Organizational Affiliation: 

Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, 8 College Rd., 169857, Singapore.

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (3D View)
Global Stoichiometry: Hetero 720-mer - A240B240C240 

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

Macromolecule Content

• Total Structure Weight: 483.12 kDa 
• Atom Count: 31,120 
• Modelled Residue Count: 4,072 
• Deposited Residue Count: 4,404 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CAPSID PROTEIN	A, D, G, J	253	Barmah Forest virus	Mutation(s): 0  EC: 3.4.21.90 Membrane Entity: Yes
UniProt
Find proteins for P89946 (Barmah forest virus) Explore P89946  Go to UniProtKB:  P89946

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
E1 ENVELOPE GLYCOPROTEIN	B, E, H, K	427	Barmah Forest virus	Mutation(s): 0  EC: 3.4.21.90 Membrane Entity: Yes
UniProt
Find proteins for P89946 (Barmah forest virus) Explore P89946  Go to UniProtKB:  P89946

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
E2 ENVELOPE GLYCOPROTEIN	C, F, I, L	421	Barmah Forest virus	Mutation(s): 0  EC: 3.4.21.90 Membrane Entity: Yes
UniProt
Find proteins for P89946 (Barmah forest virus) Explore P89946  Go to UniProtKB:  P89946

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 5.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	EMAN
RECONSTRUCTION	MPSA

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-18 
Deposition Author(s): Kostyuchenko, V.A., Jakana, J., Liu, X., Haddow, A.D., Aung, M., Weaver, S.C., Chiu, W., Lok, S.M.

Revision History  

• Version 1.0: 2012-04-18
  Type: Initial release
  
• Version 1.1: 2013-03-20
  Changes: Other
• Version 1.2: 2017-08-23
  Changes: Data collection
• Version 1.3: 2019-10-23
  Changes: Data collection, Other