[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitleThe small GTPase Ran defines nuclear pore complex asymmetry.
Journal, issue, pagesCell, Vol. 188, Issue 21, Page 5931-5946.e16, Year 2025
Publish dateOct 16, 2025
AuthorsJenny Sachweh / Mandy Börmel / Sven Klumpe / Anja Becker / Reiya Taniguchi / Marta Anna Kubańska / Verena Pintschovius / Eva Kaindl / Jürgen M Plitzko / Florian Wilfling / Martin Beck / Bernhard Hampoelz /
PubMed AbstractNuclear pore complexes (NPCs) bridge across the nuclear envelope and mediate nucleocytoplasmic exchange. They consist of hundreds of nucleoporin building blocks and exemplify the structural ...Nuclear pore complexes (NPCs) bridge across the nuclear envelope and mediate nucleocytoplasmic exchange. They consist of hundreds of nucleoporin building blocks and exemplify the structural complexity of macromolecular assemblies. To ensure transport directionality, different nucleoporin complexes are attached to the cytoplasmic and nuclear face of the NPC. How those asymmetric structures are faithfully assembled onto the symmetric scaffold architecture that exposes the same interaction surfaces to either side remained enigmatic. Here, we combine cryo-electron tomography, subtomogram averaging, and template matching with live imaging to address this question in budding yeast and Drosophila. We genetically induce ectopic nuclear pores and show that pores outside the nuclear envelope are symmetric. We furthermore demonstrate that the peripheral NPC configuration is affected by the nucleotide state of the small GTPase Ran. Our findings indicate that the nuclear transport system is self-regulatory, namely that the same molecular mechanism controls both transport and transport channel composition.
External linksCell / PubMed:40829587
MethodsEM (subtomogram averaging)
Resolution31.1 - 69.0 Å
Structure data

EMDB-53721: Asymmetric unit of the NE-NPC in S. cerevisiae Not4 deletion Nup188::GFP Nup170::mars cells
Method: EM (subtomogram averaging) / Resolution: 37.3 Å

EMDB-53722: Cytoplasmic ring asymmetric unit of the NE-NPC in S. cerevisiae Not4 deletion Nup188::GFP Nup170::mars cells
Method: EM (subtomogram averaging) / Resolution: 44.0 Å

EMDB-53723: Inner ring asymmetric unit of the NE-NPC in S. cerevisiae Not4 deletion Nup188::GFP Nup170::mars cells
Method: EM (subtomogram averaging) / Resolution: 35.3 Å

EMDB-53724: Nuclear ring asymmetric unit of the NE-NPC in S. cerevisiae Not4 deletion Nup188::GFP Nup170::mars cells
Method: EM (subtomogram averaging) / Resolution: 46.4 Å

EMDB-53725: Asymmetric unit of the nNPC in S. cerevisiae Not4 deletion Nup188::GFP Nup170::mars cells
Method: EM (subtomogram averaging) / Resolution: 39.2 Å

EMDB-53727: Top nuclear ring asymmetric unit of the nNPC in S. cerevisiae Not4 deletion Nup188::GFP Nup170::mars cells
Method: EM (subtomogram averaging) / Resolution: 38.3 Å

EMDB-53728: Inner ring asymmetric unit of the nNPC in S. cerevisiae Not4 deletion Nup188::GFP Nup170::mars cells
Method: EM (subtomogram averaging) / Resolution: 36.8 Å

EMDB-53729: Bottom nuclear ring asymmetric unit of the nNPC in S. cerevisiae Not4 deletion Nup188::GFP Nup170::mars cells
Method: EM (subtomogram averaging) / Resolution: 39.9 Å

EMDB-53731: Nuclear pore complex in the nuclear envelope (NE-NPC) in S. cerevisiae Not4 deletion Nup188::GFP Nup170::mars cells, composite structure
Method: EM (subtomogram averaging) / Resolution: 35.5 Å

EMDB-53732: Nuclear pore complex in nucleoplasmic membranes (nNPC) in S. cerevisiae Not4 deletion Nup188::GFP Nup170::mars cells, composite structure
Method: EM (subtomogram averaging) / Resolution: 36.8 Å

EMDB-53739: Asymmetric unit of the NE-NPC in D. melanogaster Nup358::VN/Nup358::VC cells
Method: EM (subtomogram averaging) / Resolution: 40.2 Å

EMDB-53740: Cytoplasmic ring asymmetric unit of the NE-NPC in D. melanogaster Nup358::VN/Nup358::VC cells
Method: EM (subtomogram averaging) / Resolution: 34.5 Å

EMDB-53741: Inner ring asymmetric unit of the NE-NPC in D. melanogaster Nup358::VN/Nup358::VC cells
Method: EM (subtomogram averaging) / Resolution: 31.1 Å

EMDB-53742: Nuclear ring asymmetric unit of the NE-NPC in D. melanogaster Nup358::VN/Nup358::VC cells
Method: EM (subtomogram averaging) / Resolution: 34.5 Å

EMDB-53743: Nuclear basket asymmetric unit of the NE-NPC in D. melanogaster Nup358::VN/Nup358::VC cells
Method: EM (subtomogram averaging) / Resolution: 43.9 Å

EMDB-53744: Asymmetric unit of the cNPC in D. melanogaster Nup358::VN/Nup358::VC cells
Method: EM (subtomogram averaging) / Resolution: 69.0 Å

EMDB-53745: Top cytoplasmic ring asymmetric unit of the cNPC in D. melanogaster Nup358::VN/Nup358::VC cells
Method: EM (subtomogram averaging) / Resolution: 50.8 Å

EMDB-53746: Inner ring asymmetric unit of the cNPC in D. melanogaster Nup358::VN/Nup358::VC cells
Method: EM (subtomogram averaging) / Resolution: 37.1 Å

EMDB-53747: Bottom cytoplasmic ring asymmetric unit of the cNPC in D. melanogaster Nup358::VN/Nup358::VC cells
Method: EM (subtomogram averaging) / Resolution: 46.0 Å

EMDB-53750: Nuclear pore complex in the nuclear envelope (NE-NPC) in D. melanogaster Nup358::VN/Nup358::VC cells, composite structure
Method: EM (subtomogram averaging) / Resolution: 31.1 Å

EMDB-53751: Nuclear pore complex in cytoplasmic membranes (cNPC) in D. melanogaster Nup358::VN/Nup358::VC cells, composite structure
Method: EM (subtomogram averaging) / Resolution: 37.1 Å

Source
  • Saccharomyces cerevisiae (brewer's yeast)
  • Drosophila melanogaster (fruit fly)

+
About Yorodumi Papers

-
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://pdbjlvh1.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 Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more