7YX3

Structure of the Mimivirus genomic fibre in its compact 6-start helix form


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

The giant mimivirus 1.2 Mb genome is elegantly organized into a 30-nm diameter helical protein shield.

Villalta, A.Schmitt, A.Estrozi, L.F.Quemin, E.R.J.Alempic, J.M.Lartigue, A.Prazak, V.Belmudes, L.Vasishtan, D.Colmant, A.M.G.Honore, F.A.Coute, Y.Grunewald, K.Abergel, C.

(2022) Elife 11

  • DOI: https://doi.org/10.7554/eLife.77607
  • Primary Citation of Related Structures:  
    7PTV, 7YX3, 7YX4, 7YX5

  • PubMed Abstract: 

    Mimivirus is the prototype of the Mimiviridae family of giant dsDNA viruses. Little is known about the organization of the 1.2 Mb genome inside the membrane-limited nucleoid filling the ~0.5 µm icosahedral capsids. Cryo-electron microscopy, cryo-electron tomography, and proteomics revealed that it is encased into a ~30-nm diameter helical protein shell surprisingly composed of two GMC-type oxidoreductases, which also form the glycosylated fibrils decorating the capsid. The genome is arranged in 5- or 6-start left-handed super-helices, with each DNA-strand lining the central channel. This luminal channel of the nucleoprotein fiber is wide enough to accommodate oxidative stress proteins and RNA polymerase subunits identified by proteomics. Such elegant supramolecular organization would represent a remarkable evolutionary strategy for packaging and protecting the genome, in a state ready for immediate transcription upon unwinding in the host cytoplasm. The parsimonious use of the same protein in two unrelated substructures of the virion is unexpected for a giant virus with thousand genes at its disposal.


  • Organizational Affiliation

    Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative GMC-type oxidoreductase
A, B
702Acanthamoeba polyphaga mimivirusMutation(s): 0 
UniProt
Find proteins for Q5UPL2 (Acanthamoeba polyphaga mimivirus)
Explore Q5UPL2 
Go to UniProtKB:  Q5UPL2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5UPL2
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union832601
Agence Nationale de la Recherche (ANR)FranceANR-16-CE11-0033-01
German Research Foundation (DFG)GermanyINST 152/772-1|152/774-1|152/775-1|152/776-1
Wellcome TrustUnited Kingdom107806/Z/15/Z
German Federal Ministry for Education and ResearchGermany05K18BHA
Alexander von Humboldt FoundationGermanyFRA 1200789 HFST-P
Agence Nationale de la Recherche (ANR)FranceANR-10-INBS-04

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-10
    Type: Initial release
  • Version 2.0: 2023-07-12
    Type: Coordinate replacement
    Reason: Model orientation/position
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description, Structure summary
  • Version 2.1: 2023-07-19
    Changes: Database references