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- EMDB-54655: Cytoplasmic ring segment of the A. thaliana nuclear pore complex -

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Basic information

Entry
Database: EMDB / ID: EMD-54655
TitleCytoplasmic ring segment of the A. thaliana nuclear pore complex
Map datamap
Sample
  • Complex: Nuclear pore complex
Keywordsnuclear pore complex / NUCLEAR PROTEIN / MEMBRANE PROTEIN
Biological speciesArabidopsis thaliana (thale cress)
Methodsubtomogram averaging / cryo EM / Resolution: 33.0 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: Ingrid Berenice Sanchez Carrillo / Patrick C Hoffmann / Agnieszka Obarska-Kosinska / Victor Fourcassié / Martin Beck / Hugo Germain /
Abstract: The nucleus is enclosed by the nuclear envelope, which contains nuclear pore complexes (NPCs). While NPCs have been well studied in vertebrates, yeast and algae, in situ structural data for higher ...The nucleus is enclosed by the nuclear envelope, which contains nuclear pore complexes (NPCs). While NPCs have been well studied in vertebrates, yeast and algae, in situ structural data for higher plants is lacking. Here we show that individual nucleoporins of Arabidopsis thaliana and humans exhibit high structural similarity. We report an in situ NPC structure of higher plants, derived from A. thaliana root protoplasts using cryo-electron tomography, subtomogram averaging and homology-based integrative modelling. We present the AtNPC model based on predictions of A. thaliana nucleoporins (NUPs), supported by mass spectrometry. Here the AtNPC scaffold contains one Y-complex ring at the cytosolic and two at the nuclear ring. The AtNPC contains prominent NUP155 connector elements that are conserved in human NPCs but not in Chlamydomonas reinhardtii NPCs. Our model suggests that the ELYS homologue HOS1 plays an important role in the head-to-tail connection of Y-complexes in AtNPCs.
History
DepositionAug 5, 2025-
Header (metadata) releaseNov 5, 2025-
Map releaseNov 5, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54655.png

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Map

FileDownload / File: emd_54655.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
8.7 Å/pix.
x 100 pix.
= 870. Å		8.7 Å/pix.
x 100 pix.
= 870. Å		8.7 Å/pix.
x 100 pix.
= 870. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 8.7 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.085
Minimum - Maximum-0.2702061 - 0.38284177
Average (Standard dev.)0.00055004086 (±0.03521669)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 870.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: halfmap1

Fileemd_54655_half_map_1.map
Annotationhalfmap1
Projections & Slices
AxesZYX

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Half map: halfmap2

Fileemd_54655_half_map_2.map
Annotationhalfmap2
Projections & Slices
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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: 33.0 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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