[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 mechanism of angiogenin activation by the ribosome.
Journal, issue, pagesNature, Vol. 630, Issue 8017, Page 769-776, Year 2024
Publish dateMay 8, 2024
AuthorsAnna B Loveland / Cha San Koh / Robin Ganesan / Allan Jacobson / Andrei A Korostelev /
PubMed AbstractAngiogenin, an RNase-A-family protein, promotes angiogenesis and has been implicated in cancer, neurodegenerative diseases and epigenetic inheritance. After activation during cellular stress, ...Angiogenin, an RNase-A-family protein, promotes angiogenesis and has been implicated in cancer, neurodegenerative diseases and epigenetic inheritance. After activation during cellular stress, angiogenin cleaves tRNAs at the anticodon loop, resulting in translation repression. However, the catalytic activity of isolated angiogenin is very low, and the mechanisms of the enzyme activation and tRNA specificity have remained a puzzle. Here we identify these mechanisms using biochemical assays and cryogenic electron microscopy (cryo-EM). Our study reveals that the cytosolic ribosome is the activator of angiogenin. A cryo-EM structure features angiogenin bound in the A site of the 80S ribosome. The C-terminal tail of angiogenin is rearranged by interactions with the ribosome to activate the RNase catalytic centre, making the enzyme several orders of magnitude more efficient in tRNA cleavage. Additional 80S-angiogenin structures capture how tRNA substrate is directed by the ribosome into angiogenin's active site, demonstrating that the ribosome acts as the specificity factor. Our findings therefore suggest that angiogenin is activated by ribosomes with a vacant A site, the abundance of which increases during cellular stress. These results may facilitate the development of therapeutics to treat cancer and neurodegenerative diseases.
External linksNature / PubMed:38718836
MethodsEM (single particle)
Resolution2.8 - 3.9 Å
Structure data

EMDB-44457: 80S ribosome with angiogenin and ternary complex in rabbit reticulocyte lysates
Method: EM (single particle) / Resolution: 3.36 Å

EMDB-44458: 80S ribosome with angiogenin, in vitro assembled complex without substrate tRNA
Method: EM (single particle) / Resolution: 3.04 Å

EMDB-44459: 80S ribosome with H13A angiogenin
Method: EM (single particle) / Resolution: 2.8 Å

EMDB-44460: 80S ribosome with H13A angiogenin and tRNA
Method: EM (single particle) / Resolution: 3.9 Å

44461

9bdl

EMDB-44461, PDB-9bdl:
80S ribosome with angiogenin
Method: EM (single particle) / Resolution: 2.8 Å

44463

9bdn

EMDB-44463, PDB-9bdn:
80S ribosome with angiogenin and tRNAAla
Method: EM (single particle) / Resolution: 3.1 Å

44464

9bdp

EMDB-44464, PDB-9bdp:
80S ribosome bound with angiogenin and complex of eEF1A and Ala-tRNAAla
Method: EM (single particle) / Resolution: 3.7 Å

Source
  • oryctolagus cuniculus (rabbit)
  • homo sapiens (human)
  • escherichia coli (E. coli)
  • saccharomyces cerevisiae (brewer's yeast)
  • escherichia coli k-12 (bacteria)
KeywordsRIBOSOME / Angiogenin / RNase

+
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