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- EMDB-25818: CryoEM map of the cytoplasmic ring of the nuclear pore complex fr... -

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Basic information

Entry
Database: EMDB / ID: EMD-25818
TitleCryoEM map of the cytoplasmic ring of the nuclear pore complex from Xenopus laevis
Map dataCryo-EM map of the cytoplasmic ring of the Nuclear pore complex from Xenopus laevis.
Sample
  • Complex: Cytoplasmic ring of Nuclear Pore Complex
KeywordsNuclear pore complex / NUCLEAR PROTEIN
Biological speciesXenopus laevis (African clawed frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.9 Å
AuthorsFontana P / Wu H
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Science / Year: 2022
Title: Structure of cytoplasmic ring of nuclear pore complex by integrative cryo-EM and AlphaFold
Authors: Fontana P / Wu H
History
DepositionDec 29, 2021-
Header (metadata) releaseJun 29, 2022-
Map releaseJun 29, 2022-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25818.png

Downloads & links

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Map

FileDownload / File: emd_25818.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of the cytoplasmic ring of the Nuclear pore complex from Xenopus laevis.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.8 Å/pix.
x 800 pix.
= 2240. Å		2.8 Å/pix.
x 800 pix.
= 2240. Å		2.8 Å/pix.
x 800 pix.
= 2240. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.8 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.24
Minimum - Maximum-0.4534166 - 5.7946024
Average (Standard dev.)0.0076423855 (±0.079009846)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions800800800
Spacing800800800
CellA=B=C: 2240.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Cytoplasmic ring of Nuclear Pore Complex

EntireName: Cytoplasmic ring of Nuclear Pore Complex
Components
  • Complex: Cytoplasmic ring of Nuclear Pore Complex

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Supramolecule #1: Cytoplasmic ring of Nuclear Pore Complex

SupramoleculeName: Cytoplasmic ring of Nuclear Pore Complex / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Xenopus laevis (African clawed frog)

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.25 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

3103

Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 333214
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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