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- EMDB-44372: In-cell Saccharomyces cerevisiae nuclear pore complex with single... -

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Basic information

Entry
Database: EMDB / ID: EMD-44372
TitleIn-cell Saccharomyces cerevisiae nuclear pore complex with single nuclear ring
Map dataYeast NPC with single nuclear ring
Sample
  • Cell: In-cell Saccharomyces cerevisiae nuclear pore complex with single nuclear ring
KeywordsNuclear envelope / Nuclear pore / Nucleocytoplasmic transport / STRUCTURAL PROTEIN
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsubtomogram averaging / cryo EM / Resolution: 30.0 Å
AuthorsSingh D / Hutchings J / Villa E
Funding support United States, European Union, 4 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
Damon Runyon Cancer Research FoundationDRG-2364-19 United States
European Molecular Biology Organization (EMBO)ALTF 871-2020European Union
National Institutes of Health/National Institute on Aging (NIH/NIA)K99AG080112 United States
CitationJournal: Cell / Year: 2024
Title: The molecular architecture of the nuclear basket.
Authors: Digvijay Singh / Neelesh Soni / Joshua Hutchings / Ignacia Echeverria / Farhaz Shaikh / Madeleine Duquette / Sergey Suslov / Zhixun Li / Trevor van Eeuwen / Kelly Molloy / Yi Shi / Junjie ...Authors: Digvijay Singh / Neelesh Soni / Joshua Hutchings / Ignacia Echeverria / Farhaz Shaikh / Madeleine Duquette / Sergey Suslov / Zhixun Li / Trevor van Eeuwen / Kelly Molloy / Yi Shi / Junjie Wang / Qiang Guo / Brian T Chait / Javier Fernandez-Martinez / Michael P Rout / Andrej Sali / Elizabeth Villa /
Abstract: The nuclear pore complex (NPC) is the sole mediator of nucleocytoplasmic transport. Despite great advances in understanding its conserved core architecture, the peripheral regions can exhibit ...The nuclear pore complex (NPC) is the sole mediator of nucleocytoplasmic transport. Despite great advances in understanding its conserved core architecture, the peripheral regions can exhibit considerable variation within and between species. One such structure is the cage-like nuclear basket. Despite its crucial roles in mRNA surveillance and chromatin organization, an architectural understanding has remained elusive. Using in-cell cryo-electron tomography and subtomogram analysis, we explored the NPC's structural variations and the nuclear basket across fungi (yeast; S. cerevisiae), mammals (mouse; M. musculus), and protozoa (T. gondii). Using integrative structural modeling, we computed a model of the basket in yeast and mammals that revealed how a hub of nucleoporins (Nups) in the nuclear ring binds to basket-forming Mlp/Tpr proteins: the coiled-coil domains of Mlp/Tpr form the struts of the basket, while their unstructured termini constitute the basket distal densities, which potentially serve as a docking site for mRNA preprocessing before nucleocytoplasmic transport.
History
DepositionApr 1, 2024-
Header (metadata) releaseAug 21, 2024-
Map releaseAug 21, 2024-
UpdateOct 2, 2024-
Current statusOct 2, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44372.png

Downloads & links

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Map

FileDownload / File: emd_44372.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationYeast NPC with single nuclear ring
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
10 Å/pix.
x 224 pix.
= 2240. Å		10 Å/pix.
x 224 pix.
= 2240. Å		10 Å/pix.
x 224 pix.
= 2240. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 10 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 483.0
Minimum - Maximum0.0 - 1023.0
Average (Standard dev.)104.384249999999994 (±180.885480000000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 2240.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Consensus C8-symmetrized map for Yeast NPC with single nuclear ring.

Fileemd_44372_additional_1.map
AnnotationConsensus C8-symmetrized map for Yeast NPC with single nuclear ring.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : In-cell Saccharomyces cerevisiae nuclear pore complex with single...

EntireName: In-cell Saccharomyces cerevisiae nuclear pore complex with single nuclear ring
Components
  • Cell: In-cell Saccharomyces cerevisiae nuclear pore complex with single nuclear ring

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Supramolecule #1: In-cell Saccharomyces cerevisiae nuclear pore complex with single...

SupramoleculeName: In-cell Saccharomyces cerevisiae nuclear pore complex with single nuclear ring
type: cell / ID: 1 / Parent: 0
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: 6.8
VitrificationCryogen name: ETHANE-PROPANE / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3708 pixel / Average electron dose: 4.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 6.0 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: C8 (8 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 30.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 21935
ExtractionNumber tomograms: 1602 / Number images used: 5160
Final angle assignmentType: MAXIMUM LIKELIHOOD

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