[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

TitleStructures of the Catalytically Activated Yeast Spliceosome Reveal the Mechanism of Branching.
Journal, issue, pagesCell, Vol. 177, Issue 2, Page 339-351.e13, Year 2019
Publish dateApr 4, 2019
AuthorsRuixue Wan / Rui Bai / Chuangye Yan / Jianlin Lei / Yigong Shi /
PubMed AbstractPre-mRNA splicing is executed by the spliceosome. Structural characterization of the catalytically activated complex (B) is pivotal for understanding the branching reaction. In this study, we ...Pre-mRNA splicing is executed by the spliceosome. Structural characterization of the catalytically activated complex (B) is pivotal for understanding the branching reaction. In this study, we assembled the B complexes on two different pre-mRNAs from Saccharomyces cerevisiae and determined the cryo-EM structures of four distinct B complexes at overall resolutions of 2.9-3.8 Å. The duplex between U2 small nuclear RNA (snRNA) and the branch point sequence (BPS) is discretely away from the 5'-splice site (5'SS) in the three B complexes that are devoid of the step I splicing factors Yju2 and Cwc25. Recruitment of Yju2 into the active site brings the U2/BPS duplex into the vicinity of 5'SS, with the BPS nucleophile positioned 4 Å away from the catalytic metal M2. This analysis reveals the functional mechanism of Yju2 and Cwc25 in branching. These structures on different pre-mRNAs reveal substrate-specific conformations of the spliceosome in a major functional state.
External linksCell / PubMed:30879786
MethodsEM (single particle)
Resolution2.9 - 3.86 Å
Structure data

EMDB-0684:
Cryo-EM structure of the catalytic activated yeast spliceosome (B* complex) assembled on ACT1 pre-mRNA at 2.9 angstrom resolution
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-0685:
Cryo-EM structure of the catalytic activated yeast spliceosome (B* complex) assembled on UBC4 pre-mRNA at 3.2 angstrom resolution
Method: EM (single particle) / Resolution: 3.2 Å

0686

6j6g

EMDB-0686, PDB-6j6g:
Cryo-EM structure of the yeast B*-a2 complex at an average resolution of 3.2 angstrom
Method: EM (single particle) / Resolution: 3.2 Å

0687

6j6h

EMDB-0687, PDB-6j6h:
Cryo-EM structure of the yeast B*-a1 complex at an average resolution of 3.6 angstrom
Method: EM (single particle) / Resolution: 3.6 Å

0691

6j6n

EMDB-0691, PDB-6j6n:
Cryo-EM structure of the yeast B*-b1 complex at an average resolution of 3.86 angstrom
Method: EM (single particle) / Resolution: 3.86 Å

0692

6j6q

EMDB-0692, PDB-6j6q:
Cryo-EM structure of the yeast B*-b2 complex at an average resolution of 3.7 angstrom
Method: EM (single particle) / Resolution: 3.7 Å

Chemicals

ChemComp-IHP:
INOSITOL HEXAKISPHOSPHATE / Phytic acid

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

ChemComp-MG:
Unknown entry

ChemComp-ZN:
Unknown entry

Source
  • saccharomyces cerevisiae s288c (yeast)
  • Baker's yeast (brewer's yeast)
  • saccharomyces cerevisiae (strain atcc 204508 / s288c) (yeast)
KeywordsSPLICING / spliceosme / B* complex / branching / snRNP / U snRNA / spliceosome

+
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