6ZQW

Cryo-EM structure of immature Spondweni virus


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Flavivirus maturation leads to the formation of an occupied lipid pocket in the surface glycoproteins.

Renner, M.Dejnirattisai, W.Carrique, L.Martin, I.S.Karia, D.Ilca, S.L.Ho, S.F.Kotecha, A.Keown, J.R.Mongkolsapaya, J.Screaton, G.R.Grimes, J.M.

(2021) Nat Commun 12: 1238-1238

  • DOI: https://doi.org/10.1038/s41467-021-21505-9
  • Primary Citation of Related Structures:  
    6ZQI, 6ZQJ, 6ZQU, 6ZQV, 6ZQW

  • PubMed Abstract: 

    Flaviviruses such as Dengue (DENV) or Zika virus (ZIKV) assemble into an immature form within the endoplasmatic reticulum (ER), and are then processed by furin protease in the trans-Golgi. To better grasp maturation, we carry out cryo-EM reconstructions of immature Spondweni virus (SPOV), a human flavivirus of the same serogroup as ZIKV. By employing asymmetric localised reconstruction we push the resolution to 3.8 Å, enabling us to refine an atomic model which includes the crucial furin protease recognition site and a conserved Histidine pH-sensor. For direct comparison, we also solve structures of the mature forms of SPONV and DENV to 2.6 Å and 3.1 Å, respectively. We identify an ordered lipid that is present in only the mature forms of ZIKV, SPOV, and DENV and can bind as a consequence of rearranging amphipathic stem-helices of E during maturation. We propose a structural role for the pocket and suggest it stabilizes mature E.


  • Organizational Affiliation

    Division of Structural Biology, The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Genome polyproteinA,
C [auth D],
E [auth G]
505Spondweni virusMutation(s): 0 
UniProt
Find proteins for C8XPB6 (Spondweni virus)
Explore C8XPB6 
Go to UniProtKB:  C8XPB6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC8XPB6
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
prM169Spondweni virusMutation(s): 0 
UniProt
Find proteins for C8XPB6 (Spondweni virus)
Explore C8XPB6 
Go to UniProtKB:  C8XPB6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC8XPB6
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom060208/Z/00/Z
Wellcome TrustUnited Kingdom093305/Z/10/Z
Wellcome TrustUnited Kingdom204703/Z/16/Z
Wellcome TrustUnited Kingdom200835/Z/16/Z
Wellcome TrustUnited Kingdom203141/Z/16/Z

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-20
    Type: Initial release
  • Version 1.1: 2021-08-04
    Changes: Database references