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- EMDB-53723: Inner ring asymmetric unit of the NE-NPC in S. cerevisiae Not4 de... -

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Basic information

Entry
Database: EMDB / ID: EMD-53723
TitleInner ring asymmetric unit of the NE-NPC in S. cerevisiae Not4 deletion Nup188::GFP Nup170::mars cells
Map data
Sample
  • Organelle or cellular component: Inner ring, Nuclear pore complex (NE-NPC)
KeywordsInner ring / NPC / Nuclear Pore Complex / Yeast / TRANSPORT PROTEIN
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsubtomogram averaging / cryo EM / Resolution: 35.3 Å
AuthorsSachweh J / Beck M
Funding support Germany, European Union, 3 items
OrganizationGrant numberCountry
Hessian Ministry of Science, Higher Education and Art (HMWK)EnABLE Germany
European Research Council (ERC)724379-Complex AssemblyEuropean Union
European Research Council (ERC)101054823-NPCvalveEuropean Union
CitationJournal: Cell / Year: 2025
Title: The small GTPase Ran defines nuclear pore complex asymmetry.
Authors: Jenny Sachweh / Mandy Börmel / Sven Klumpe / Anja Becker / Reiya Taniguchi / Marta Anna Kubańska / Verena Pintschovius / Eva Kaindl / Jürgen M Plitzko / Florian Wilfling / Martin Beck / Bernhard Hampoelz /
Abstract: Nuclear pore complexes (NPCs) bridge across the nuclear envelope and mediate nucleocytoplasmic exchange. They consist of hundreds of nucleoporin building blocks and exemplify the structural ...Nuclear pore complexes (NPCs) bridge across the nuclear envelope and mediate nucleocytoplasmic exchange. They consist of hundreds of nucleoporin building blocks and exemplify the structural complexity of macromolecular assemblies. To ensure transport directionality, different nucleoporin complexes are attached to the cytoplasmic and nuclear face of the NPC. How those asymmetric structures are faithfully assembled onto the symmetric scaffold architecture that exposes the same interaction surfaces to either side remained enigmatic. Here, we combine cryo-electron tomography, subtomogram averaging, and template matching with live imaging to address this question in budding yeast and Drosophila. We genetically induce ectopic nuclear pores and show that pores outside the nuclear envelope are symmetric. We furthermore demonstrate that the peripheral NPC configuration is affected by the nucleotide state of the small GTPase Ran. Our findings indicate that the nuclear transport system is self-regulatory, namely that the same molecular mechanism controls both transport and transport channel composition.
History
DepositionMay 14, 2025-
Header (metadata) releaseAug 27, 2025-
Map releaseAug 27, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53723.png

Downloads & links

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Map

FileDownload / File: emd_53723.map.gz / Format: CCP4 / Size: 5.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
8.7 Å/pix.
x 110 pix.
= 957.44 Å		8.7 Å/pix.
x 110 pix.
= 957.44 Å		8.7 Å/pix.
x 110 pix.
= 957.44 Å

Surface

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Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 8.704 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.16
Minimum - Maximum-0.6045815 - 0.7436796
Average (Standard dev.)-0.0018148139 (±0.06606618)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions110110110
Spacing110110110
CellA=B=C: 957.44006 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53723_msk_1.map
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AxesZYX

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Half map: Halfmap used for FSC calculation

Fileemd_53723_half_map_1.map
AnnotationHalfmap used for FSC calculation
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: Halfmap used for FSC calculation

Fileemd_53723_half_map_2.map
AnnotationHalfmap used for FSC calculation
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Inner ring, Nuclear pore complex (NE-NPC)

EntireName: Inner ring, Nuclear pore complex (NE-NPC)
Components
  • Organelle or cellular component: Inner ring, Nuclear pore complex (NE-NPC)

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Supramolecule #1: Inner ring, Nuclear pore complex (NE-NPC)

SupramoleculeName: Inner ring, Nuclear pore complex (NE-NPC) / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Details: Inner ring asymmetric unit of the NE-NPC in S. cerevisiae Not4 deletion Nup188::GFP Nup170::mars cells
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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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: 7
GridModel: Quantifoil R1/4 / Material: GOLD / Mesh: 200 / Support film - Material: SILICON DIOXIDE / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 293 K / Instrument: LEICA EM GP
DetailsLiquid cultures, OD600 of 0.3-0.8, synthetic complete (SD) medium with 2% glucose

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 2.5 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: 2.0 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: 35.3 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: novaSTA / Number subtomograms used: 1776
ExtractionNumber tomograms: 40 / Number images used: 281 / Software - Name: novaSTA
CTF correctionType: PHASE FLIPPING ONLY
Final angle assignmentType: OTHER / Software - Name: novaSTA
FSC plot (resolution estimation)

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