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- EMDB-31531: Twofold block reconstruction of the Melbournevirus capsid -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-31531
TitleTwofold block reconstruction of the Melbournevirus capsid
Map dataTwofold block reconstruction of Melbournevirus
Sample
  • Virus: Melbournevirus
Biological speciesMelbournevirus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.43 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-
UpdateJul 20, 2022-
Current statusJul 20, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_31531.png

Downloads & links

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Map

FileDownload / File: emd_31531.map.gz / Format: CCP4 / Size: 1.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTwofold block reconstruction of Melbournevirus
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.21 Å/pix.
x 700 pix.
= 1547. Å		2.21 Å/pix.
x 700 pix.
= 1547. Å		2.21 Å/pix.
x 700 pix.
= 1547. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.21 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.09316524 - 0.122904554
Average (Standard dev.)0.0003968342 (±0.00513245)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions700700700
Spacing700700700
CellA=B=C: 1547.0 Å
α=β=γ: 90.0 °

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Supplemental data

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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
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 26.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.43 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 187440
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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