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- PDB-7yx3: Structure of the Mimivirus genomic fibre in its compact 6-start h... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7yx3 | ||||||||||||||||||||||||
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Title | Structure of the Mimivirus genomic fibre in its compact 6-start helix form | ||||||||||||||||||||||||
![]() | Putative GMC-type oxidoreductase | ||||||||||||||||||||||||
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Function / homology | ![]() oxidoreductase activity, acting on CH-OH group of donors / ![]() Similarity search - Function | ||||||||||||||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||||||||||||||
Method | ![]() ![]() | ||||||||||||||||||||||||
![]() | 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. ...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 support | European Union, ![]() ![]() ![]()
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![]() | ![]() Title: The giant mimivirus 1.2 Mb genome is elegantly organized into a 30-nm diameter helical protein shield. Authors: Alejandro Villalta / Alain Schmitt / Leandro F Estrozi / Emmanuelle R J Quemin / Jean-Marie Alempic / Audrey Lartigue / Vojtěch Pražák / Lucid Belmudes / Daven Vasishtan / Agathe M G ...Authors: Alejandro Villalta / Alain Schmitt / Leandro F Estrozi / Emmanuelle R J Quemin / Jean-Marie Alempic / Audrey Lartigue / Vojtěch Pražák / Lucid Belmudes / Daven Vasishtan / Agathe M G Colmant / Flora A Honoré / Yohann Couté / Kay Grünewald / Chantal Abergel / ![]() ![]() ![]() Abstract: Mimivirus is the prototype of the 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 ...Mimivirus is the prototype of the 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. | ||||||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 226.2 KB | Display | ![]() |
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PDB format | ![]() | 186.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 14353MC ![]() 7ptvC ![]() 7yx4C ![]() 7yx5C C: citing same article ( M: map data used to model this data |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Components
#1: Protein | Mass: 77018.023 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() #2: Chemical | ![]() Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
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Sample preparation
Component | Name: Mimivirus genomic fibre in its compact 6-start helix form Type: COMPLEX / Entity ID: #1 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() ![]() ![]() |
Buffer solution | pH: 7.5 |
Buffer component | Conc.: 40 mM / Name: Tris buffer / Formula: (HOCH2)3CNH2 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() |
Vitrification![]() | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source![]() ![]() |
Electron lens | Mode: BRIGHT FIELD![]() |
Image recording | Electron dose: 50.6 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
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Processing
CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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Helical symmerty | Angular rotation/subunit: 49.43 ° / Axial rise/subunit: 20.47 Å / Axial symmetry: C3 | ||||||||||||||||||||||||
3D reconstruction![]() | Resolution: 4 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 8479 / Symmetry type: HELICAL | ||||||||||||||||||||||||
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