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- EMDB-54653: Asymmetric subunit of the A. thaliana nuclear pore complex -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-54653
TitleAsymmetric subunit of the A. thaliana nuclear pore complex
Map dataUnfiltered STA map of asymmetric SU
Sample
  • Complex: Nuclear pore complex
Keywordsnuclear pore complex / NUCLEAR PROTEIN / MEMBRANE PROTEIN
Biological speciesArabidopsis thaliana (thale cress)
Methodsubtomogram averaging / cryo EM / Resolution: 39.0 Å
AuthorsSanchez Carrillo IB / Hoffmann PC / Obarska-Kosinska A / Fourcassie V / Beck M / Germain H
Funding support Germany, European Union, 3 items
OrganizationGrant numberCountry
Max Planck Society Germany
European Research Council (ERC)101054823European Union
European Molecular Biology Organization (EMBO)ALTF 33-2021European Union
CitationJournal: Nat.Plants / Year: 2025
Title: In situ architecture of the nuclear pore complex of the higher plant Arabidopsis thaliana
Authors: Sanchez Carrillo IB / Hoffmann PC / Obarska-Kosinska A / Fourcassie V / Beck M / Germain H
History
DepositionAug 5, 2025-
Header (metadata) releaseNov 5, 2025-
Map releaseNov 5, 2025-
UpdateNov 5, 2025-
Current statusNov 5, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54653.png

Downloads & links

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Map

FileDownload / File: emd_54653.map.gz / Format: CCP4 / Size: 6.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnfiltered STA map of asymmetric SU
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
8.7 Å/pix.
x 120 pix.
= 1044. Å		8.7 Å/pix.
x 120 pix.
= 1044. Å		8.7 Å/pix.
x 120 pix.
= 1044. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 8.7 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.25923884 - 0.31194374
Average (Standard dev.)0.00060278946 (±0.043863963)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-60-60-60
Dimensions120120120
Spacing120120120
CellA=B=C: 1044.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Halfmap 1 of asymmetric SU

Fileemd_54653_half_map_1.map
AnnotationHalfmap 1 of asymmetric SU
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Halfmap 2 of asymmetric SU

Fileemd_54653_half_map_2.map
AnnotationHalfmap 2 of asymmetric SU
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Nuclear pore complex

EntireName: Nuclear pore complex
Components
  • Complex: Nuclear pore complex

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Supramolecule #1: Nuclear pore complex

SupramoleculeName: Nuclear pore complex / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 5.7
VitrificationCryogen name: ETHANE
DetailsCryo-FIB lamellae of isolated A.thaliana root protoplasts

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 2.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 39.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: novaSTA / Number subtomograms used: 632
ExtractionNumber tomograms: 37 / Number images used: 79 / Software - Name: novaSTA
CTF correctionType: PHASE FLIPPING ONLY
Final angle assignmentType: NOT APPLICABLE

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