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- EMDB-31528: Ewald sphere-corrected Melbournevirus particle -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-31528
TitleEwald sphere-corrected Melbournevirus particle
Map dataWhole Melbournevirus reconstruction
Sample
  • Virus: Melbournevirus
Biological speciesMelbournevirus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.91 Å
AuthorsBurton-Smith RN / Murata K
Funding support Japan, Sweden, 4 items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP19H04845 Japan
Swedish Research Council2018-03387 Sweden
The Swedish Foundation for Strategic ResearchJA2014-5721 Sweden
Swedish Research Council2018-00421 Sweden
CitationJournal: To Be Published
Title: The 4.4A structure of the giant Melbournevirus virion belonging to the Marseilleviridae family
Authors: Burton-Smith RN / Reddy HKN / Svenda M / Abergel C / Okamoto K / Murata K
History
DepositionJul 15, 2021-
Header (metadata) releaseJul 20, 2022-
Map releaseJul 20, 2022-
UpdateMar 1, 2023-
Current statusMar 1, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_31528.png

Downloads & links

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Map

FileDownload / File: emd_31528.map.gz / Format: CCP4 / Size: 11.1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationWhole Melbournevirus reconstruction
Voxel sizeX=Y=Z: 2.21 Å
Density
Contour LevelBy AUTHOR: 0.012
Minimum - Maximum-0.029068284 - 0.06704602
Average (Standard dev.)0.004388696 (±0.0048017213)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions144014401440
Spacing144014401440
CellA=B=C: 3182.4001 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Whole Melbournevirus reconstruction, capsid masked for easier visualisation...

Fileemd_31528_additional_1.map
AnnotationWhole Melbournevirus reconstruction, capsid masked for easier visualisation of capsid
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Melbournevirus

EntireName: Melbournevirus
Components
  • Virus: Melbournevirus

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Supramolecule #1: Melbournevirus

SupramoleculeName: Melbournevirus / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 1560514 / Sci species name: Melbournevirus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
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: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 26.4 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.91 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 3124
FSC plot (resolution estimation)

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