[English] 日本語
Yorodumi
- EMDB-10660: Nup116_delta_NPC_25C -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-10660
TitleNup116_delta_NPC_25C
Map data
Sample
  • Complex: Nuclear pore complex 116delta strain at 25C
    • Protein or peptide: Nuclear pore complex 116delta strain at 25C
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsubtomogram averaging / cryo EM / Resolution: 35.0 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 / Mulller 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) releaseMar 4, 2020-
Map releaseSep 9, 2020-
UpdateFeb 10, 2021-
Current statusFeb 10, 2021Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.11
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.11
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10660.png

Downloads & links

-
Map

FileDownload / File: emd_10660.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: 0.11 / Movie #1: 0.11
Minimum - Maximum-0.87573606 - 3.248832
Average (Standard dev.)0.0028520674 (±0.051166)
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-0.8763.2490.003

-
Supplemental data

-
Sample components

-
Entire : Nuclear pore complex 116delta strain at 25C

EntireName: Nuclear pore complex 116delta strain at 25C
Components
  • Complex: Nuclear pore complex 116delta strain at 25C
    • Protein or peptide: Nuclear pore complex 116delta strain at 25C

-
Supramolecule #1: Nuclear pore complex 116delta strain at 25C

SupramoleculeName: Nuclear pore complex 116delta strain at 25C / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Nuclear pore complex 116delta strain at 25C
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

-
Macromolecule #1: Nuclear pore complex 116delta strain at 25C

MacromoleculeName: Nuclear pore complex 116delta strain at 25C / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
SequenceString:
x

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
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

-
Image processing

Final reconstructionApplied symmetry - Point group: C8 (8 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 35.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 1300
ExtractionNumber tomograms: 145 / Number images used: 250
Final angle assignmentType: PROJECTION MATCHING

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more