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


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: https://doi.org/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 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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoprotein E1A [auth N],
D [auth T],
G [auth Z],
H [auth a]
439Sindbis virusMutation(s): 0 
UniProt
Find proteins for A0A3G2BZ29 (Sindbis virus)
Explore A0A3G2BZ29 
Go to UniProtKB:  A0A3G2BZ29
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3G2BZ29
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoprotein E2B [auth P],
E [auth V],
I [auth d],
J [auth e]
388Sindbis virusMutation(s): 0 
UniProt
Find proteins for A0A3G2BZ29 (Sindbis virus)
Explore A0A3G2BZ29 
Go to UniProtKB:  A0A3G2BZ29
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3G2BZ29
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Assembly protein E3C [auth R],
F [auth X],
K [auth h],
L [auth i]
69Sindbis virusMutation(s): 0 
UniProt
Find proteins for A0A3G2BZ29 (Sindbis virus)
Explore A0A3G2BZ29 
Go to UniProtKB:  A0A3G2BZ29
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3G2BZ29
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8K6
Query on 8K6

Download Ideal Coordinates CCD File 
M [auth d]Octadecane
C18 H38
RZJRJXONCZWCBN-UHFFFAOYSA-N
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  (Full details and data files)

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