6IMM

Cryo-EM structure of an alphavirus, Sindbis virus


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Implication for alphavirus host-cell entry and assembly indicated by a 3.5 angstrom resolution cryo-EM structure.

Chen, L.Wang, M.Zhu, D.Sun, Z.Ma, J.Wang, J.Kong, L.Wang, S.Liu, Z.Wei, L.He, Y.Wang, J.Zhang, X.

(2018) Nat Commun 9: 5326-5326

  • DOI: 10.1038/s41467-018-07704-x

  • PubMed Abstract: 
  • Alphaviruses are enveloped RNA viruses that contain several human pathogens. Due to intrinsic heterogeneity of alphavirus particles, a high resolution structure of the virion is currently lacking. Here we provide a 3.5 Å cryo-EM structure of Sindbis ...

    Alphaviruses are enveloped RNA viruses that contain several human pathogens. Due to intrinsic heterogeneity of alphavirus particles, a high resolution structure of the virion is currently lacking. Here we provide a 3.5 Å cryo-EM structure of Sindbis virus, using block based reconstruction method that overcomes the heterogeneity problem. Our structural analysis identifies a number of conserved residues that play pivotal roles in the virus life cycle. We identify a hydrophobic pocket in the subdomain D of E2 protein that is stabilized by an unknown pocket factor near the viral membrane. Residues in the pocket are conserved in different alphaviruses. The pocket strengthens the interactions of the E1/E2 heterodimer and may facilitate virus assembly. Our study provides structural insights into alphaviruses that may inform the design of drugs and vaccines.


    Organizational Affiliation

    National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, People's Republic of China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Spike glycoprotein E1
N, T, Z, a
439Sindbis virusMutation(s): 0 
EC: 3.4.21.90
Find proteins for A0A3G2BZ29 (Sindbis virus)
Go to UniProtKB:  A0A3G2BZ29
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Spike glycoprotein E2
P, V, d, e
388Sindbis virusMutation(s): 0 
EC: 3.4.21.90
Find proteins for A0A3G2BZ29 (Sindbis virus)
Go to UniProtKB:  A0A3G2BZ29
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Assembly protein E3
R, X, h, i
69Sindbis virusMutation(s): 0 
EC: 3.4.21.90
Find proteins for A0A3G2BZ29 (Sindbis virus)
Go to UniProtKB:  A0A3G2BZ29
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8K6
Query on 8K6

Download SDF File 
Download CCD File 
d
Octadecane
N-Octadecane
C18 H38
RZJRJXONCZWCBN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-03-13
    Type: Initial release