6ZQW | pdb_00006zqw

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

Validation slider image for 6ZQW

This is version 1.3 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 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.

Macromolecule Content 

  • Total Structure Weight: 279.6 kDa 
  • Atom Count: 15,096 
  • Modeled Residue Count: 1,965 
  • Deposited Residue Count: 2,529 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Genome polyproteinA,
C [auth D],
E [auth G]
505Spondweni virusMutation(s): 0 
UniProt
Find proteins for A0ACD6B8C5 (Spondweni virus)
Explore A0ACD6B8C5 
Go to UniProtKB:  A0ACD6B8C5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0ACD6B8C5
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
prM169Spondweni virusMutation(s): 0 
UniProt
Find proteins for A0ACD6B8C5 (Spondweni virus)
Explore A0ACD6B8C5 
Go to UniProtKB:  A0ACD6B8C5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0ACD6B8C5
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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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
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION3.1

Structure Validation

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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
  • Version 1.2: 2024-10-23
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.3: 2025-07-02
    Changes: Data collection