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- EMDB-61557: palisade lattice of mpox virus -

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Basic information

Entry
Database: EMDB / ID: EMD-61557
Titlepalisade lattice of mpox virus
Map datalowpass filtered and C3 symmetrized map for display
Sample
  • Virus: Monkeypox virus
Keywordspalisade protein on monkeypox virus core / VIRAL PROTEIN
Biological speciesMonkeypox virus
Methodsubtomogram averaging / cryo EM / Resolution: 26.8 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) releaseNov 6, 2024-
Map releaseNov 6, 2024-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61557.png

Downloads & links

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Map

FileDownload / File: emd_61557.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationlowpass filtered and C3 symmetrized map for display
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.44 Å/pix.
x 128 pix.
= 696.32 Å		5.44 Å/pix.
x 128 pix.
= 696.32 Å		5.44 Å/pix.
x 128 pix.
= 696.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.44 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0
Minimum - Maximum-17.708029 - 10.577674
Average (Standard dev.)-0.17398989 (±1.1788201)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 696.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_61557_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: original average result without lowpass filter

Fileemd_61557_additional_1.map
Annotationoriginal average result without lowpass filter
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_61557_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_61557_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

MicroscopeTFS 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: 26.8 Å / Resolution method: FSC 0.143 CUT-OFF
Details: resolution is estimated in dynamo using dfsc function. mask was used for fsc calculation.
Number subtomograms used: 10502
ExtractionNumber tomograms: 105 / Number images used: 24495
Final angle assignmentType: OTHER

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