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- EMDB-14353: Structure of the Mimivirus genomic fibre in its compact 6-start h... -

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Basic information

Entry
Database: EMDB / ID: EMD-14353
TitleStructure of the Mimivirus genomic fibre in its compact 6-start helix form
Map datapostprocessed masked map
Sample
  • Complex: Mimivirus genomic fibre in its compact 6-start helix form
    • Protein or peptide: Putative GMC-type oxidoreductase
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDEFlavin adenine dinucleotide
KeywordsMimivirus / Genomic fibre / Cytoplasmic infectious cycle / 1.2 Mb dsDNA / VIRUS / VIRAL PROTEIN
Function / homology
Function and homology information


oxidoreductase activity, acting on CH-OH group of donors / flavin adenine dinucleotide binding
Similarity search - Function
GMC oxidoreductases signature 2. / Glucose-methanol-choline oxidoreductase / Glucose-methanol-choline oxidoreductase, N-terminal / GMC oxidoreductase / Glucose-methanol-choline oxidoreductase, C-terminal / GMC oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Putative GMC-type oxidoreductase
Similarity search - Component
Biological speciesAcanthamoeba polyphaga mimivirus
Methodhelical reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsVillalta A / Schmitt A
Funding supportEuropean Union, France, Germany, United Kingdom, 7 items
OrganizationGrant numberCountry
European Research Council (ERC)832601European Union
Agence Nationale de la Recherche (ANR)ANR-16-CE11-0033-01 France
German Research Foundation (DFG)INST 152/772-1|152/774-1|152/775-1|152/776-1 Germany
Wellcome Trust107806/Z/15/Z United Kingdom
German Federal Ministry for Education and Research05K18BHA Germany
Alexander von Humboldt FoundationFRA 1200789 HFST-P Germany
Agence Nationale de la Recherche (ANR)ANR-10-INBS-04 France
CitationJournal: Elife / Year: 2022
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
DepositionFeb 15, 2022-
Header (metadata) releaseAug 10, 2022-
Map releaseAug 10, 2022-
UpdateJul 19, 2023-
Current statusJul 19, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14353.png

Downloads & links

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Map

FileDownload / File: emd_14353.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationpostprocessed masked map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 400 pix.
= 436. Å		1.09 Å/pix.
x 400 pix.
= 436. Å		1.09 Å/pix.
x 400 pix.
= 436. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0165
Minimum - Maximum-0.0388897 - 0.086372234
Average (Standard dev.)0.0006199821 (±0.0040113702)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 436.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unmasked map before postprocessing

Fileemd_14353_additional_1.map
AnnotationUnmasked map before postprocessing
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unmasked half map

Fileemd_14353_half_map_1.map
AnnotationUnmasked half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unmasked half map

Fileemd_14353_half_map_2.map
AnnotationUnmasked half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Mimivirus genomic fibre in its compact 6-start helix form

EntireName: Mimivirus genomic fibre in its compact 6-start helix form
Components
  • Complex: Mimivirus genomic fibre in its compact 6-start helix form
    • Protein or peptide: Putative GMC-type oxidoreductase
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDEFlavin adenine dinucleotide

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Supramolecule #1: Mimivirus genomic fibre in its compact 6-start helix form

SupramoleculeName: Mimivirus genomic fibre in its compact 6-start helix form
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Acanthamoeba polyphaga mimivirus / Strain: Reunion

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Macromolecule #1: Putative GMC-type oxidoreductase

MacromoleculeName: Putative GMC-type oxidoreductase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Acanthamoeba polyphaga mimivirus
Molecular weightTheoretical: 77.018023 KDa
SequenceString: MKNRECCKCY NPCEKICVNY STTDVAFERP NPCKPTPCKP TPIPCDPCHN TKDNLTGDIV IIGAGAAGSL LAHYLARFSN MKIILLEAG HSHFNDPVVT DPMGFFGKYN PPNENISMSQ NPSYSWQGAQ EPNTGAYGNR PIIAHGMGFG GSTMINRLNL V VGGRTVFD ...String:
MKNRECCKCY NPCEKICVNY STTDVAFERP NPCKPTPCKP TPIPCDPCHN TKDNLTGDIV IIGAGAAGSL LAHYLARFSN MKIILLEAG HSHFNDPVVT DPMGFFGKYN PPNENISMSQ NPSYSWQGAQ EPNTGAYGNR PIIAHGMGFG GSTMINRLNL V VGGRTVFD NDWPVGWKYD DVKNYFRRVL VDINPVRDNT KASITSVALD ALRIIAEQQI ASGEPVDFLL NKATGNVPNV EK TTPDAVP LNLNDYEGVN SVVAFSSFYM GVNQLSDGNY IRKYAGNTYL NRNYVDENGR GIGKFSGLRV VSDAVVDRII FKG NRAVGV NYIDREGIMH YVKVNKEVVV TSGAFYTPTI LQRSGIGDFT YLSSIGVKNL VYNNPLVGTG LKNHYSPVTI TRVH GEPSE VSRFLSNMAA NPTNMGFKGL AELGFHRLDP NKPANANTVT YRKYQLMMTA GVGIPAEQQY LSGLSPSSNN LFTLI ADDI RFAPEGYIKI GTPNIPRDVP KIFFNTFVTY TPTSAPADQQ WPIAQKTLAP LISALLGYDI IYQTLISMNQ TARDSG FQV SLEMVYPLND LIYKLHNGLA TYGANWWHYF VPTLVGDDTP AGREFADTLS KLSYYPRVGA HLDSHQGCSC SIGRTVD SN LKVIGTQNVR VADLSAAAFP PGGNTWATAS MIGARAVDLI LGFPYLRDLP VNDVPILNVN

UniProtKB: Putative GMC-type oxidoreductase

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Macromolecule #2: FLAVIN-ADENINE DINUCLEOTIDE

MacromoleculeName: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 2 / Number of copies: 2 / Formula: FAD
Molecular weightTheoretical: 785.55 Da
Chemical component information

ChemComp-FAD:
FLAVIN-ADENINE DINUCLEOTIDE / FAD*YM / Flavin adenine dinucleotide

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.5 / Component - Concentration: 40.0 mM / Component - Formula: (HOCH2)3CNH2 / Component - Name: Tris buffer
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 50.6 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Featureless cylinder
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Helical parameters - Δz: 20.47 Å
Applied symmetry - Helical parameters - Δ&Phi: 49.43 °
Applied symmetry - Helical parameters - Axial symmetry: C3 (3 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 8479
FSC plot (resolution estimation)

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