[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

TitleStructure and Conformational Dynamics of the Human Spliceosomal B Complex.
Journal, issue, pagesCell, Vol. 172, Issue 3, Page 454-464.e11, Year 2018
Publish dateJan 25, 2018
AuthorsDavid Haselbach / Ilya Komarov / Dmitry E Agafonov / Klaus Hartmuth / Benjamin Graf / Olexandr Dybkov / Henning Urlaub / Berthold Kastner / Reinhard Lührmann / Holger Stark /
PubMed AbstractThe spliceosome is a highly dynamic macromolecular complex that precisely excises introns from pre-mRNA. Here we report the cryo-EM 3D structure of the human B spliceosome at 3.4 Å resolution. In ...The spliceosome is a highly dynamic macromolecular complex that precisely excises introns from pre-mRNA. Here we report the cryo-EM 3D structure of the human B spliceosome at 3.4 Å resolution. In the B state, the spliceosome is activated but not catalytically primed, so that it is functionally blocked prior to the first catalytic step of splicing. The spliceosomal core is similar to the yeast B spliceosome; important differences include the presence of the RNA helicase aquarius and peptidyl prolyl isomerases. To examine the overall dynamic behavior of the purified spliceosome, we developed a principal component analysis-based approach. Calculating the energy landscape revealed eight major conformational states, which we refined to higher resolution. Conformational differences of the highly flexible structural components between these eight states reveal how spliceosomal components contribute to the assembly of the spliceosome, allowing it to generate a dynamic interaction network required for its subsequent catalytic activation.
External linksCell / PubMed:29361316
MethodsEM (single particle)
Resolution3.4 - 16.0 Å
Structure data

EMDB-4233:
Human Bact spliceosome state 1 unmasked
Method: EM (single particle) / Resolution: 16.0 Å

EMDB-4234:
Human Bact spliceosome state 2 unmasked
Method: EM (single particle) / Resolution: 16.0 Å

EMDB-4235:
Human Bact spliceosome state 3 unmasked
Method: EM (single particle) / Resolution: 11.3 Å

EMDB-4236:
Human Bact spliceosome state 4 unmasked
Method: EM (single particle) / Resolution: 6.7 Å

EMDB-4237:
Human Bact spliceosome state 5 unmasked
Method: EM (single particle) / Resolution: 6.2 Å

EMDB-4238:
Human Bact spliceosome state 6 unmasked
Method: EM (single particle) / Resolution: 8.1 Å

EMDB-4239:
Human Bact spliceosome state 7 unmasked
Method: EM (single particle) / Resolution: 10.8 Å

4240

6ff7

EMDB-4240: Human Bact spliceosome state 8 unmasked
PDB-6ff7: human Bact spliceosome core structure
Method: EM (single particle) / Resolution: 4.5 Å

EMDB-4247:
Human Bact spliceosome state 1 core
Method: EM (single particle) / Resolution: 16.0 Å

EMDB-4248:
Human Bact spliceosome state 2 core
Method: EM (single particle) / Resolution: 4.5 Å

EMDB-4249:
Human Bact spliceosome state 3 core
Method: EM (single particle) / Resolution: 6.5 Å

EMDB-4250:
Human Bact spliceosome state 4 core
Method: EM (single particle) / Resolution: 3.9 Å

EMDB-4251:
Human Bact spliceosome state 5 core
Method: EM (single particle) / Resolution: 4.1 Å

EMDB-4252:
Human Bact spliceosome state 6 core
Method: EM (single particle) / Resolution: 4.5 Å

EMDB-4253:
Human Bact spliceosome state 7 core
Method: EM (single particle) / Resolution: 6.1 Å

EMDB-4254:
Human Bact spliceosome state 8 core
Method: EM (single particle) / Resolution: 3.7 Å

4255

6ff4

EMDB-4255, PDB-6ff4:
human Bact spliceosome core structure
Method: EM (single particle) / Resolution: 3.4 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-IHP:
INOSITOL HEXAKISPHOSPHATE / Phytic acid

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

ChemComp-ZN:
Unknown entry

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM / Adenosine diphosphate

Source
  • homo sapiens (human)
  • Human (human)
KeywordsSPLICING / spliceosome / human / HELA / BACT / dynamics

+
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