6IMM

Cryo-EM structure of an alphavirus, Sindbis virus


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report



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
  • Primary Citation of Related Structures:  
    6IMM

  • 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

    University of Chinese Academy of Sciences, 100049, Beijing, People's Republic of China. xzzhang@ibp.ac.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Spike glycoprotein E1NTZa439Sindbis virusMutation(s): 0 
EC: 3.4.21.90
Find proteins for A0A3G2BZ29 (Sindbis virus)
Explore A0A3G2BZ29 
Go to UniProtKB:  A0A3G2BZ29
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Spike glycoprotein E2PVde388Sindbis virusMutation(s): 0 
EC: 3.4.21.90
Find proteins for A0A3G2BZ29 (Sindbis virus)
Explore A0A3G2BZ29 
Go to UniProtKB:  A0A3G2BZ29
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Assembly protein E3RXhi69Sindbis virusMutation(s): 0 
EC: 3.4.21.90
Find proteins for A0A3G2BZ29 (Sindbis virus)
Explore A0A3G2BZ29 
Go to UniProtKB:  A0A3G2BZ29
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8K6
Query on 8K6

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

Experimental Data

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

Structure Validation

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Entry History 

Deposition Data

Revision History 

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