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 1.0 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: 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 ...

    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

    Aix-Marseille University, CNRS-AMU UMR7256, Marseille, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Putative GMC-type oxidoreductaseA, B702Acanthamoeba polyphaga mimivirusMutation(s): 0 
UniProt
Find proteins for A0A8A5IZP6 (Mimivirus reunion)
Explore A0A8A5IZP6 
Go to UniProtKB:  A0A8A5IZP6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8A5IZP6
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD (Subject of Investigation/LOI)
Query on FAD

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
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