[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

TitleMolecular basis for the activation of human spliceosome.
Journal, issue, pagesNat Commun, Vol. 15, Issue 1, Page 6348, Year 2024
Publish dateJul 27, 2024
AuthorsXiechao Zhan / Yichen Lu / Yigong Shi /
PubMed AbstractThe spliceosome executes pre-mRNA splicing through four sequential stages: assembly, activation, catalysis, and disassembly. Activation of the spliceosome, namely remodeling of the pre-catalytic ...The spliceosome executes pre-mRNA splicing through four sequential stages: assembly, activation, catalysis, and disassembly. Activation of the spliceosome, namely remodeling of the pre-catalytic spliceosome (B complex) into the activated spliceosome (B complex) and the catalytically activated spliceosome (B complex), involves major flux of protein components and structural rearrangements. Relying on a splicing inhibitor, we have captured six intermediate states between the B and B complexes: pre-B, B-I, B-II, B-III, B-IV, and post-B. Their cryo-EM structures, together with an improved structure of the catalytic step I spliceosome (C complex), reveal how the catalytic center matures around the internal stem loop of U6 snRNA, how the branch site approaches 5'-splice site, how the RNA helicase PRP2 rearranges to bind pre-mRNA, and how U2 snRNP undergoes remarkable movement to facilitate activation. We identify a previously unrecognized key role of PRP2 in spliceosome activation. Our study recapitulates a molecular choreography of the human spliceosome during its catalytic activation.
External linksNat Commun / PubMed:39068178 / PubMed Central
MethodsEM (single particle)
Resolution3.0 - 4.2 Å
Structure data

35105

8i0p

EMDB-35105, PDB-8i0p:
The cryo-EM structure of human pre-Bact complex
Method: EM (single particle) / Resolution: 3.4 Å

35107

8i0r

EMDB-35107, PDB-8i0r:
The cryo-EM structure of human Bact-I complex
Method: EM (single particle) / Resolution: 3.0 Å

35108

8i0s

EMDB-35108, PDB-8i0s:
The cryo-EM structure of human Bact-II complex
Method: EM (single particle) / Resolution: 4.2 Å

35109

8i0t

EMDB-35109, PDB-8i0t:
The cryo-EM structure of human Bact-III complex
Method: EM (single particle) / Resolution: 3.0 Å

35110

8i0u

EMDB-35110, PDB-8i0u:
The cryo-EM structure of human Bact-IV complex
Method: EM (single particle) / Resolution: 3.3 Å

35111

8i0v

EMDB-35111, PDB-8i0v:
The cryo-EM structure of human post-Bact complex
Method: EM (single particle) / Resolution: 3.0 Å

35113

8i0w

EMDB-35113, PDB-8i0w:
The cryo-EM structure of human C complex
Method: EM (single particle) / Resolution: 3.4 Å

Chemicals

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

ChemComp-MG:
Unknown entry

ChemComp-ZN:
Unknown entry

ChemComp-IHP:
INOSITOL HEXAKISPHOSPHATE

Source
  • homo sapiens (human)
  • unidentified adenovirus
KeywordsSPLICING / spliceosome / pre-Bact complex / RNA splicing / PRP2 / activation / Bact-I complex / Bact-II complex / branching / Bact complex / PRP16

+
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