[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 basis of archaeal FttA-dependent transcription termination.
Journal, issue, pagesNature, Year 2024
Publish dateSep 25, 2024
AuthorsLinlin You / Chengyuan Wang / Vadim Molodtsov / Konstantin Kuznedelov / Xinyi Miao / Breanna R Wenck / Paul Ulisse / Travis J Sanders / Craig J Marshall / Emre Firlar / Jason T Kaelber / Thomas J Santangelo / Richard H Ebright /
PubMed AbstractThe ribonuclease FttA (also known as aCPSF and aCPSF1) mediates factor-dependent transcription termination in archaea. Here we report the structure of a Thermococcus kodakarensis transcription pre- ...The ribonuclease FttA (also known as aCPSF and aCPSF1) mediates factor-dependent transcription termination in archaea. Here we report the structure of a Thermococcus kodakarensis transcription pre-termination complex comprising FttA, Spt4, Spt5 and a transcription elongation complex (TEC). The structure shows that FttA interacts with the TEC in a manner that enables RNA to proceed directly from the TEC RNA-exit channel to the FttA catalytic centre and that enables endonucleolytic cleavage of RNA by FttA, followed by 5'→3' exonucleolytic cleavage of RNA by FttA and concomitant 5'→3' translocation of FttA on RNA, to apply mechanical force to the TEC and trigger termination. The structure further reveals that Spt5 bridges FttA and the TEC, explaining how Spt5 stimulates FttA-dependent termination. The results reveal functional analogy between bacterial and archaeal factor-dependent termination, functional homology between archaeal and eukaryotic factor-dependent termination, and fundamental mechanistic similarities in factor-dependent termination in bacteria, archaea, and eukaryotes.
External linksNature / PubMed:39322680
MethodsEM (single particle)
Resolution2.2 - 2.67 Å
Structure data

44438

9bct

EMDB-44438, PDB-9bct:
Cryo-EM structure of Thermococcus kodakarensis FttA-dependent transcription pre-termination complex containing 44 nt RNA
Method: EM (single particle) / Resolution: 2.5 Å

44439

9bcu

EMDB-44439, PDB-9bcu:
Cryo-EM structure of Thermococcus kodakarensis FttA-dependent transcription pre-termination complex containing 52 nt RNA
Method: EM (single particle) / Resolution: 2.2 Å

EMDB-44454: Cryo-EM structure of Thermococcus kodakarensis FttA-dependent transcription pre-termination complex containing 44 nt RNA
Method: EM (single particle) / Resolution: 2.5 Å

EMDB-44455: Cryo-EM structure of Thermococcus kodakarensis FttA-dependent transcription pre-termination complex containing 52 nt RNA
Method: EM (single particle) / Resolution: 2.2 Å

EMDB-44649: Cryo-EM structure of Thermococcus kodakarensis FttA-dependent transcription pre-termination complex containing 44 nt RNA (local refinement map)
Method: EM (single particle) / Resolution: 2.67 Å

EMDB-44650: Cryo-EM structure of Thermococcus kodakarensis FttA-dependent transcription pre-termination complex containing 52 nt RNA (local refinement map)
Method: EM (single particle) / Resolution: 2.34 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-ZN:
Unknown entry

Source
  • thermococcus kodakarensis (archaea)
  • synthetic construct (others)
KeywordsTRANSCRIPTION / RNA polymerase / pre-termination complex / FttA / archaea

+
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