7YX3

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

• PDB DOI:  https://doi.org/10.2210/pdb7YX3/pdb
• EM Map EMD-14353: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Acanthamoeba polyphaga mimivirus
• Mutation(s): No 


• Deposited: 2022-02-15 Released: 2022-08-10 
• Deposition Author(s): 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.
• Funding Organization(s): European Research Council (ERC), Agence Nationale de la Recherche (ANR), German Research Foundation (DFG), Wellcome Trust, German Federal Ministry for Education and Research, Alexander von Humboldt Foundation

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Experimental Data Snapshot

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

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

• PubMed: 35900198 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (3D View)
Global Stoichiometry: Homo 18-mer - A18 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 155.61 kDa 
• Atom Count: 10,124 
• Modelled Residue Count: 1,298 
• Deposited Residue Count: 1,404 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative GMC-type oxidoreductase	A, B	702	Acanthamoeba polyphaga mimivirus	Mutation(s): 0  Gene Names: MIMI_R135 EC: 1
UniProt
Find proteins for Q5UPL2 (Acanthamoeba polyphaga mimivirus) Explore Q5UPL2  Go to UniProtKB:  Q5UPL2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD (Subject of Investigation/LOI)	C [auth A], D [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N

Experimental Data & Validation

Experimental Data

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-08-10 
Deposition Author(s): 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.

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Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	832601
Agence Nationale de la Recherche (ANR)	France	ANR-16-CE11-0033-01
German Research Foundation (DFG)	Germany	INST 152/772-1|152/774-1|152/775-1|152/776-1
Wellcome Trust	United Kingdom	107806/Z/15/Z
German Federal Ministry for Education and Research	Germany	05K18BHA
Alexander von Humboldt Foundation	Germany	FRA 1200789 HFST-P
Agence Nationale de la Recherche (ANR)	France	ANR-10-INBS-04

Revision History  

• 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