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- EMDB-10661: Nup116delta_NPC_37C -

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Basic information

Entry
Database: EMDB / ID: EMD-10661
TitleNup116delta_NPC_37C
Map data
Sample
  • Complex: Nuclear pore complex Nup116k.o. shifted at 37C
    • Protein or peptide: Nuclear pore complex 116delta strain at 37C
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsubtomogram averaging / cryo EM / Resolution: 50.0 Å
AuthorsAllegretti M / Zimmerli CE / Rantos V / Wilfling F / Ronchi P / Fung HKH / Lee C-W / Hagen W / Turonova B / Karius K ...Allegretti M / Zimmerli CE / Rantos V / Wilfling F / Ronchi P / Fung HKH / Lee C-W / Hagen W / Turonova B / Karius K / Zhang X / Muller C / Schwab Y / Mahamid J / Pfander B / Kosinski J / Beck M
Funding support Germany, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)Complex Assembly Germany
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
DepositionFeb 4, 2020-
Header (metadata) releaseSep 9, 2020-
Map releaseSep 9, 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: 0.052
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.052
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10661.png

Downloads & links

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Map

FileDownload / File: emd_10661.map.gz / Format: CCP4 / Size: 11.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 13.8 Å
Density
Contour LevelBy AUTHOR: 0.052 / Movie #1: 0.052
Minimum - Maximum-0.17147166 - 0.4571286
Average (Standard dev.)0.0010865658 (±0.016670536)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions144144144
Spacing144144144
CellA=B=C: 1987.2001 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z13.813.813.8
M x/y/z144144144
origin x/y/z0.0000.0000.000
length x/y/z1987.2001987.2001987.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS144144144
D min/max/mean-0.1710.4570.001

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Supplemental data

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Sample components

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Entire : Nuclear pore complex Nup116k.o. shifted at 37C

EntireName: Nuclear pore complex Nup116k.o. shifted at 37C
Components
  • Complex: Nuclear pore complex Nup116k.o. shifted at 37C
    • Protein or peptide: Nuclear pore complex 116delta strain at 37C

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Supramolecule #1: Nuclear pore complex Nup116k.o. shifted at 37C

SupramoleculeName: Nuclear pore complex Nup116k.o. shifted at 37C / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Nuclear pore complex Nup116k.o. shifted at 37C
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Nuclear pore complex 116delta strain at 37C

MacromoleculeName: Nuclear pore complex 116delta strain at 37C / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
x

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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) / 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
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: 50.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 55
ExtractionNumber tomograms: 70 / Number images used: 60
Final angle assignmentType: PROJECTION MATCHING

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