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- EMDB-61555: sub-tomogram average structure of monkeypox virus palisade -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-61555
Titlesub-tomogram average structure of monkeypox virus palisade
Map datamasked map of MPXV STA for final display
Sample
  • Virus: Monkeypox virus
Keywordspalisade protein on monkeypox virus core / VIRAL PROTEIN
Biological speciesMonkeypox virus
Methodsubtomogram averaging / cryo EM / Resolution: 11.45 Å
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_61555.png

Downloads & links

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Map

FileDownload / File: emd_61555.map.gz / Format: CCP4 / Size: 2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmasked map of MPXV STA for final display
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.72 Å/pix.
x 80 pix.
= 217.6 Å		2.72 Å/pix.
x 80 pix.
= 217.6 Å		2.72 Å/pix.
x 80 pix.
= 217.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.72 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0
Minimum - Maximum-8.253838 - 13.047463
Average (Standard dev.)0.046488296 (±0.6937558)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions808080
Spacing808080
CellA=B=C: 217.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_61555_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: unmasked map of MPXV palisade STA

Fileemd_61555_additional_1.map
Annotationunmasked map of MPXV palisade STA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_61555_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_61555_half_map_2.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 : 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
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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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 reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 11.45 Å / Resolution method: FSC 0.143 CUT-OFF
Details: gold-standard refinement was applied in dynamo using dynamo plugin. two half maps were generated in relion4 using 2D reconstruction and the final map obtained was sharpened in relion4. FSC ...Details: gold-standard refinement was applied in dynamo using dynamo plugin. two half maps were generated in relion4 using 2D reconstruction and the final map obtained was sharpened in relion4. FSC curve was calculated using dfsc function in dynamo and resolution estimate is based on 0.143 cut-off.
Number subtomograms used: 16074
ExtractionNumber tomograms: 105 / Number images used: 24495
Final angle assignmentType: OTHER

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