[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

TitleStructural framework for the assembly of the human tRNA ligase complex.
Journal, issue, pagesNat Commun, Vol. 17, Issue 1, Year 2026
Publish dateSep 17, 2026
AuthorsMoritz M Pfleiderer / Moritz Kleinwächter / Ajse S Nievergelt / Franziska M Boneberg / Alena Kroupova / Javier Martinez / Martin Jinek /
PubMed AbstractIn human cells, a subset of tRNA-encoding genes contain introns. These are removed by a spliceosome-independent pathway in which the tRNA splicing endonuclease complex catalyzes intron excision. The ...In human cells, a subset of tRNA-encoding genes contain introns. These are removed by a spliceosome-independent pathway in which the tRNA splicing endonuclease complex catalyzes intron excision. The resulting exons are subsequently ligated by the tRNA-ligase complex (tRNA-LC), comprising Ashwin, CGI-99, FAM98B, DDX1, and RTCB/HSPC117. The molecular architecture and functions of its non-catalytic subunits remain poorly understood. Using cryo-EM, we determined an atomic-resolution structure of human tRNA-LC. CGI-99, DDX1, and FAM98B form an α-helical bundle that contacts RTCB opposite its active site and anchors DDX1 via its C-terminal helix. FAM98B and CGI-99 form an extensively co-folded heterodimer that clamps Ashwin in a pincer-like structure. Structure-based mutagenesis supports the architecture of the complex. We further show that FAM98A and FAM98C assemble distinct RTCB-containing complexes lacking Ashwin, suggesting specialized cellular functions. Our results provide insights into the molecular assembly of the tRNA ligase complex, highlighting its functions in tRNA biogenesis and beyond.
External linksNat Commun / PubMed:42754576 / PubMed Central
MethodsEM (single particle)
Resolution3.3 Å
Structure data

58360

31fw

EMDB-58360, PDB-31fw:
Human tRNA ligase complex
Method: EM (single particle) / Resolution: 3.3 Å

Chemicals

ChemComp-MG:
Unknown entry

Source
  • homo sapiens (human)
  • aequorea victoria (jellyfish)
KeywordsLIGASE / tRNA

+
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