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- EMDB-52158: Nuclear ring of the nuclear pore complex from Nup133-deficient mo... -

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Basic information

Entry
Database: EMDB / ID: EMD-52158
TitleNuclear ring of the nuclear pore complex from Nup133-deficient mouse embryonic stem cell
Map dataNuclear ring of the nuclear pore complex from Nup133-deficient mouse embryonic stem cell
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: 33.4 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: To Be Published
Title: Nuclear pores safeguard the integrity of the nuclear envelope
Authors: Taniguchi R / Orniacki C / Kreysing JP / Zila V / Zimmerli CE / Boehm S / Turonova B / Kraeusslich H-G / Doye V / Beck M
History
DepositionNov 20, 2024-
Header (metadata) releaseJan 22, 2025-
Map releaseJan 22, 2025-
UpdateJan 22, 2025-
Current statusJan 22, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52158.png

Downloads & links

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Map

FileDownload / File: emd_52158.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNuclear ring of the nuclear pore complex from Nup133-deficient mouse embryonic stem cell
Projections & slices

Image control

Size
Brightness
Contrast
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)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 10.728 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.4548583 - 0.69395065
Average (Standard dev.)0.00038070543 (±0.07366234)
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_52158_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of the nuclear ring of the...

Fileemd_52158_half_map_1.map
AnnotationHalf map of the nuclear ring of the nuclear pore complex from Nup133-deficient mouse embryonic stem cell
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of the nuclear ring of the...

Fileemd_52158_half_map_2.map
AnnotationHalf map of the nuclear ring of the nuclear pore complex from Nup133-deficient mouse embryonic stem cell
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: 33.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: novaSTA / Number subtomograms used: 970
ExtractionNumber tomograms: 123 / Number images used: 2510
Final angle assignmentType: OTHER / Software - Name: novaSTA
FSC plot (resolution estimation)

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