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- EMDB-61560: regularly-shaped mpox mature virus -

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Basic information

Entry
Database: EMDB / ID: EMD-61560
Titleregularly-shaped mpox mature virus
Map datatomogram of a representative irregularly-shaped mpox mature virus
Sample
  • Virus: Monkeypox virus
Keywordspalisade protein on monkeypox virus core / VIRAL PROTEIN
Biological speciesMonkeypox virus
Methodelectron tomography / cryo EM
AuthorsHong Y / Huang B / Zhang J / Peng C / Kong W / Tan W / Li S
Funding support China, 3 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)#82241066 China
National Science Foundation (NSF, China)#32241031 China
National Science Foundation (NSF, China)#32171195 China
CitationJournal: Cell Discov / Year: 2024
Title: Molecular architecture of monkeypox mature virus.
Authors: Ye Hong / Baoying Huang / Junxia Zhang / Cheng Peng / Weizheng Kong / Wenjie Tan / Sai Li /
History
DepositionSep 16, 2024-
Header (metadata) releaseOct 30, 2024-
Map releaseOct 30, 2024-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61560.png

Downloads & links

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Map

FileDownload / File: emd_61560.map.gz / Format: CCP4 / Size: 2.5 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationtomogram of a representative irregularly-shaped mpox mature virus
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.44 Å/pix.
x 450 pix.
= 2448. Å		5.44 Å/pix.
x 1440 pix.
= 7833.6 Å		5.44 Å/pix.
x 1024 pix.
= 5570.56 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 5.44 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-217.09584000000001 - 160.285249999999991
Average (Standard dev.)2.997357 (±7.5562563)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin0-153178
Dimensions14401024450
Spacing10241440450
CellA: 5570.56 Å / B: 7833.6 Å / C: 2448.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Monkeypox virus

EntireName: Monkeypox virus
Components
  • Virus: Monkeypox virus

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Supramolecule #1: Monkeypox virus

SupramoleculeName: Monkeypox virus / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 10244 / Sci species name: Monkeypox virus / Sci species strain: Clade IIb / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE
SectioningOther: NO SECTIONING

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 3.94 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.5 µm / Nominal defocus min: 2.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber images used: 35

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