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- EMDB-10198: In-cell S cerevisiae nuclear pore complex -

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Basic information

Entry
Database: EMDB / ID: EMD-10198
TitleIn-cell S cerevisiae nuclear pore complex
Map data
Sample
  • Complex: S cerevisiae nuclear pore complex
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsubtomogram averaging / cryo EM / Resolution: 25.0 Å
AuthorsBeck M / Allegretti M
CitationJournal: Nature / Year: 2020
Title: In-cell architecture of the nuclear pore and snapshots of its turnover.
Authors: Matteo Allegretti / Christian E Zimmerli / Vasileios Rantos / Florian Wilfling / Paolo Ronchi / Herman K H Fung / Chia-Wei Lee / Wim Hagen / Beata Turoňová / Kai Karius / Mandy Börmel / ...Authors: Matteo Allegretti / Christian E Zimmerli / Vasileios Rantos / Florian Wilfling / Paolo Ronchi / Herman K H Fung / Chia-Wei Lee / Wim Hagen / Beata Turoňová / Kai Karius / Mandy Börmel / Xiaojie Zhang / Christoph W Müller / Yannick Schwab / Julia Mahamid / Boris Pfander / Jan Kosinski / Martin Beck /
Abstract: Nuclear pore complexes (NPCs) fuse the inner and outer membranes of the nuclear envelope. They comprise hundreds of nucleoporins (Nups) that assemble into multiple subcomplexes and form large central ...Nuclear pore complexes (NPCs) fuse the inner and outer membranes of the nuclear envelope. They comprise hundreds of nucleoporins (Nups) that assemble into multiple subcomplexes and form large central channels for nucleocytoplasmic exchange. How this architecture facilitates messenger RNA export, NPC biogenesis and turnover remains poorly understood. Here we combine in situ structural biology and integrative modelling with correlative light and electron microscopy and molecular perturbation to structurally analyse NPCs in intact Saccharomyces cerevisiae cells within the context of nuclear envelope remodelling. We find an in situ conformation and configuration of the Nup subcomplexes that was unexpected from the results of previous in vitro analyses. The configuration of the Nup159 complex appears critical to spatially accommodate its function as an mRNA export platform, and as a mediator of NPC turnover. The omega-shaped nuclear envelope herniae that accumulate in nup116Δ cells conceal partially assembled NPCs lacking multiple subcomplexes, including the Nup159 complex. Under conditions of starvation, herniae of a second type are formed that cytoplasmically expose NPCs. These results point to a model of NPC turnover in which NPC-containing vesicles bud off from the nuclear envelope before degradation by the autophagy machinery. Our study emphasizes the importance of investigating the structure-function relationship of macromolecular complexes in their cellular context.
History
DepositionAug 7, 2019-
Header (metadata) releaseMar 18, 2020-
Map releaseAug 26, 2020-
UpdateFeb 10, 2021-
Current statusFeb 10, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0606
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0606
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10198.png

Downloads & links

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Map

FileDownload / File: emd_10198.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
6.74 Å/pix.
x 288 pix.
= 1941.12 Å		6.74 Å/pix.
x 288 pix.
= 1941.12 Å		6.74 Å/pix.
x 288 pix.
= 1941.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 6.74 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0606 / Movie #1: 0.0606
Minimum - Maximum-0.33706844 - 0.5150499
Average (Standard dev.)0.0012541794 (±0.032157622)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 1941.1199 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z6.746.746.74
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z1941.1201941.1201941.120
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-0.3370.5150.001

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Supplemental data

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Sample components

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Entire : S cerevisiae nuclear pore complex

EntireName: S cerevisiae nuclear pore complex
Components
  • Complex: S cerevisiae nuclear pore complex

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Supramolecule #1: S cerevisiae nuclear pore complex

SupramoleculeName: S cerevisiae nuclear pore complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: x
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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 4.0 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: C8 (8 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 2000
ExtractionNumber tomograms: 230 / Number images used: 4000
Final angle assignmentType: PROJECTION MATCHING

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