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- EMDB-14355: Structure of the Mimivirus genomic fibre in its relaxed 5-start h... -

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Basic information

Entry
Database: EMDB / ID: EMD-14355
TitleStructure of the Mimivirus genomic fibre in its relaxed 5-start helix form
Map dataMasked postprocessed map
Sample
  • Complex: Mimivirus genomic fibre in its relaxed 5-start helix form
    • Protein or peptide: Putative glucose-methanol-choline oxidoreductase protein
  • Ligand: FLAVIN-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 glucose-methanol-choline oxidoreductase protein
Similarity search - Component
Biological speciesAcanthamoeba polyphaga mimivirus
Methodhelical reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsVillalta A / Schmitt A
Funding support France, 7 items
OrganizationGrant numberCountry
European Research Council (ERC)832601 France
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 France
Wellcome Trust107806/Z/15/Z France
German Federal Ministry for Education and Research05K18BHA France
Alexander von Humboldt FoundationFRA 1200789 HFST-P France
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 17, 2024-
Current statusJul 17, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14355.png

Downloads & links

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Map

FileDownload / File: emd_14355.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMasked postprocessed 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: 0.017
Minimum - Maximum-0.035781518 - 0.069340274
Average (Standard dev.)0.0005898562 (±0.0037580417)
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_14355_additional_1.map
AnnotationUnmasked map before postprocessing
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unmasked half map

Fileemd_14355_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_14355_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 relaxed 5-start helix form

EntireName: Mimivirus genomic fibre in its relaxed 5-start helix form
Components
  • Complex: Mimivirus genomic fibre in its relaxed 5-start helix form
    • Protein or peptide: Putative glucose-methanol-choline oxidoreductase protein
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE

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Supramolecule #1: Mimivirus genomic fibre in its relaxed 5-start helix form

SupramoleculeName: Mimivirus genomic fibre in its relaxed 5-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 glucose-methanol-choline oxidoreductase protein

MacromoleculeName: Putative glucose-methanol-choline oxidoreductase protein
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acanthamoeba polyphaga mimivirus
Molecular weightTheoretical: 76.431055 KDa
SequenceString: MAHRSRCNCN DTSNSNGSQH GINLPLRKID TYDPCVNCRV KPHLCPKPHP CPKPENLEAD IVIIGAGAAG CVLAYYLTKF SDLKIILLE AGHTHFNDPV VTDPMGFFGK YNPPNENIRM SQNPSYAWQP ALEPDTGAYS MRNVVAHGLA VGGSTAINQL N YIVGGRTV ...String:
MAHRSRCNCN DTSNSNGSQH GINLPLRKID TYDPCVNCRV KPHLCPKPHP CPKPENLEAD IVIIGAGAAG CVLAYYLTKF SDLKIILLE AGHTHFNDPV VTDPMGFFGK YNPPNENIRM SQNPSYAWQP ALEPDTGAYS MRNVVAHGLA VGGSTAINQL N YIVGGRTV FDNDWPTGWK YDDIKKYFRR VLADISPIRD GTKVNLTNTI LESMRVLADQ QVSSGVPVDF LINKATGGLP NI EQTYQGA PIVNLNDYEG INSVCGFKSY YVGVNQLSDG SYIRKYAGNT YLNSYYVDSN GFGIGKFSNL RVISDAVVDR IHF EGQRAV SVTYIDKKGN LHSVKVHKEV EICSGSFFTP TILQRSGIGD FSYLSSIGVP DLVYNNPLVG QGLRNHYSPI TQVS VTGPD AAAFLSNTAA GPTNMSFRGA GMLGYHKLEP NKPSNAGSVT YRKYELLVTG GVAISADQQY LSGISSSTGN YFALI ADDI RFAPVGYIKI GTPNFPRDTP KIFFNTFVNY TPTTDPADQQ WPVAQKTLAP LISALLGYDA IYQIVQQMKV VAVNAG FNV TLQMAYPPND LLVELHNGLN TYGINWWHYF VPSLVNDDTP AGKLFASTLS KLSYYPRSGA HLDSHQSCSC SIGGTVD TE LKVIGVENVR VTDLSAAPHP PGGNTWCTAA MIGARATDLI LGKPLVANLP PEDVPVFTTS

UniProtKB: Putative glucose-methanol-choline oxidoreductase protein

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Macromolecule #2: FLAVIN-ADENINE DINUCLEOTIDE

MacromoleculeName: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 2 / Number of copies: 1 / Formula: FAD
Molecular weightTheoretical: 785.55 Da
Chemical component information

ChemComp-FAD:
FLAVIN-ADENINE DINUCLEOTIDE / FAD*YM

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

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 31.11 Å
Applied symmetry - Helical parameters - Δ&Phi: -23.975 °
Applied symmetry - Helical parameters - Axial symmetry: D5 (2x5 fold dihedral)
Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 11958
Startup modelType of model: OTHER / Details: Featureless cylinder
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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