[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

TitleA checkpoint function for Nup98 in nuclear pore formation suggested by novel inhibitory nanobodies.
Journal, issue, pagesEMBO J, Year 2024
Publish dateApr 22, 2024
AuthorsMireia Solà Colom / Zhenglin Fu / Philip Gunkel / Thomas Güttler / Sergei Trakhanov / Vasundara Srinivasan / Kathrin Gregor / Tino Pleiner / Dirk Görlich /
PubMed AbstractNuclear pore complex (NPC) biogenesis is a still enigmatic example of protein self-assembly. We now introduce several cross-reacting anti-Nup nanobodies for imaging intact nuclear pore complexes from ...Nuclear pore complex (NPC) biogenesis is a still enigmatic example of protein self-assembly. We now introduce several cross-reacting anti-Nup nanobodies for imaging intact nuclear pore complexes from frog to human. We also report a simplified assay that directly tracks postmitotic NPC assembly with added fluorophore-labeled anti-Nup nanobodies. During interphase, NPCs are inserted into a pre-existing nuclear envelope. Monitoring this process is challenging because newly assembled NPCs are indistinguishable from pre-existing ones. We overcame this problem by inserting Xenopus-derived NPCs into human nuclear envelopes and using frog-specific anti-Nup nanobodies for detection. We further asked whether anti-Nup nanobodies could serve as NPC assembly inhibitors. Using a selection strategy against conserved epitopes, we obtained anti-Nup93, Nup98, and Nup155 nanobodies that block Nup-Nup interfaces and arrest NPC assembly. We solved structures of nanobody-target complexes and identified roles for the Nup93 α-solenoid domain in recruiting Nup358 and the Nup214·88·62 complex, as well as for Nup155 and the Nup98 autoproteolytic domain in NPC scaffold assembly. The latter suggests a checkpoint linking pore formation to the assembly of the Nup98-dominated permeability barrier.
External linksEMBO J / PubMed:38649536
MethodsEM (single particle) / X-ray diffraction
Resolution1.41 - 4.4 Å
Structure data

14849

7zox

EMDB-14849: Nup93 in complex with 5-Nup93 inhibitory NB and 15-Nup93 tracking NB
PDB-7zox: Nup93 in complex with xhNup93-Nb4i and xNup93-Nb2t
Method: EM (single particle) / Resolution: 4.4 Å

PDB-7now:
Complex of Nucleoporin-98 and nanobody MS98-27 solved at 1.85A resolution
Method: X-RAY DIFFRACTION / Resolution: 1.85 Å

PDB-7nqa:
Crystal structure of Nucleoporin-98 nanobody MS98-6 complex solved at 2.2A resolution
Method: X-RAY DIFFRACTION / Resolution: 2.2 Å

PDB-8cds:
Crystal structure of the xhNup93-Nb4i VHH antibody
Method: X-RAY DIFFRACTION / Resolution: 1.53 Å

PDB-8cdt:
Crystal structure of the xNup93-Nb2t VHH antibody
Method: X-RAY DIFFRACTION / Resolution: 1.41 Å

PDB-8ozb:
Crystal structure of Nup35-Nb complex
Method: X-RAY DIFFRACTION / Resolution: 2.09 Å

Chemicals

ChemComp-NA:
Unknown entry

ChemComp-SO4:
SULFATE ION / Sulfate

ChemComp-HOH:
WATER / Water

ChemComp-TRS:
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / pH buffer*YM / Tris

ChemComp-EDO:
1,2-ETHANEDIOL / Ethylene glycol

ChemComp-PEG:
DI(HYDROXYETHYL)ETHER / Diethylene glycol

ChemComp-GOL:
GLYCEROL / Glycerol

Source
  • Xenopus laevis, Vicugna pacos
  • xenopus laevis (African clawed frog)
  • vicugna pacos (alpaca)
  • xenopus tropicalis (tropical clawed frog)
  • lama glama (llama)
  • homo sapiens (human)
KeywordsNUCLEAR PROTEIN / Nup98 / Nanobody / complex / NUP93 / Nuclearporin / inhibitory NB / tracking NB / IMMUNE SYSTEM / inhibitory VHH antibody / VHH antibody / TRANSPORT PROTEIN / Nuclear pore complex Nanobody

+
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://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