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- EMDB-52162: Cytoplasmic ring of the nuclear pore complex from Nup133-deficien... -

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Basic information

Entry
Database: EMDB / ID: EMD-52162
TitleCytoplasmic ring of the nuclear pore complex from Nup133-deficient neural progenitors differentiated from mES cells
Map dataCytoplasmic ring of the nuclear pore complex from Nup133-deficient neural progenitors differentiated from mES cells
Sample
  • Complex: Inner ring of the nuclear pore complex from wild-type mouse embryonic stem cell
Keywordscomplex / nuclear transport / nuclear envelope / TRANSPORT PROTEIN
Biological speciesMus musculus (house mouse)
Methodsubtomogram averaging / cryo EM / Resolution: 34.2 Å
AuthorsTaniguchi R / Beck M
Funding support Germany, European Union, 2 items
OrganizationGrant numberCountry
Max Planck Society Germany
European Research Council (ERC)101054823European Union
CitationJournal: Nat Cell Biol / Year: 2025
Title: Nuclear pores safeguard the integrity of the nuclear envelope.
Authors: Reiya Taniguchi / Clarisse Orniacki / Jan Philipp Kreysing / Vojtech Zila / Christian E Zimmerli / Stefanie Böhm / Beata Turoňová / Hans-Georg Kräusslich / Valérie Doye / Martin Beck /
Abstract: Nuclear pore complexes (NPCs) mediate nucleocytoplasmic exchange, which is essential for eukaryotes. Mutations in the central scaffolding components of NPCs are associated with genetic diseases, but ...Nuclear pore complexes (NPCs) mediate nucleocytoplasmic exchange, which is essential for eukaryotes. Mutations in the central scaffolding components of NPCs are associated with genetic diseases, but how they manifest only in specific tissues remains unclear. This is exemplified in Nup133-deficient mouse embryonic stem cells, which grow normally during pluripotency, but differentiate poorly into neurons. Here, using an innovative in situ structural biology approach, we show that Nup133 mouse embryonic stem cells have heterogeneous NPCs with non-canonical symmetries and missing subunits. During neuronal differentiation, Nup133-deficient NPCs frequently disintegrate, resulting in abnormally large nuclear envelope openings. We propose that the elasticity of the NPC scaffold has a protective function for the nuclear envelope and that its perturbation becomes critical under conditions that impose an increased mechanical load onto nuclei.
History
DepositionNov 20, 2024-
Header (metadata) releaseJan 22, 2025-
Map releaseJan 22, 2025-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52162.png

Downloads & links

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Map

FileDownload / File: emd_52162.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCytoplasmic ring of the nuclear pore complex from Nup133-deficient neural progenitors differentiated from mES cells
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
10.73 Å/pix.
x 100 pix.
= 1072.8 Å		10.73 Å/pix.
x 100 pix.
= 1072.8 Å		10.73 Å/pix.
x 100 pix.
= 1072.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 10.728 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-0.61192816 - 0.81623834
Average (Standard dev.)0.00043564907 (±0.078164354)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-50-50-50
Dimensions100100100
Spacing100100100
CellA=B=C: 1072.7999 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52162_msk_1.map
Projections & Slices
AxesZYX

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Additional map: Consensus map of the asymmetric unit of the...

Fileemd_52162_additional_1.map
AnnotationConsensus map of the asymmetric unit of the nuclear pore complex from Nup133-deficient neural progenitors differentiated from mES cells
Projections & Slices
AxesZYX

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Additional map: Composite map of the asymmetric unit of the...

Fileemd_52162_additional_2.map
AnnotationComposite map of the asymmetric unit of the nuclear pore complex from Nup133-deficient neural progenitors differentiated from mES cells
Projections & Slices
AxesZYX

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Additional map: C8-symmetrized composite map of the nuclear pore complex...

Fileemd_52162_additional_3.map
AnnotationC8-symmetrized composite map of the nuclear pore complex from Nup133-deficient neural progenitors differentiated from mES cells
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of the cytoplasmic ring of the...

Fileemd_52162_half_map_1.map
AnnotationHalf map of the cytoplasmic ring of the nuclear pore complex from Nup133-deficient neural progenitors differentiated from mES cells
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of the cytoplasmic ring of the...

Fileemd_52162_half_map_2.map
AnnotationHalf map of the cytoplasmic ring of the nuclear pore complex from Nup133-deficient neural progenitors differentiated from mES cells
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 of the nuclear pore complex from wild-type mouse embry...

EntireName: Inner ring of the nuclear pore complex from wild-type mouse embryonic stem cell
Components
  • Complex: Inner ring of the nuclear pore complex from wild-type mouse embryonic stem cell

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Supramolecule #1: Inner ring of the nuclear pore complex from wild-type mouse embry...

SupramoleculeName: Inner ring of the nuclear pore complex from wild-type mouse embryonic stem cell
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Mus musculus (house mouse) / Strain: mES HM1

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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
GridModel: Quantifoil / Material: GOLD / Mesh: 200
VitrificationCryogen name: ETHANE / Chamber humidity: 70 % / Chamber temperature: 300 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 6 / 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: 4.5 µm / Nominal defocus min: 2.5 µm
Sample stageCooling holder cryogen: NITROGEN
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: 34.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: novaSTA / Number subtomograms used: 894
ExtractionNumber tomograms: 104 / Number images used: 1073
CTF correctionSoftware - Name: NOVACTF / Type: PHASE FLIPPING ONLY
Final angle assignmentType: OTHER / Software - Name: novaSTA
FSC plot (resolution estimation)

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