[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

TitleModulation of cardiac ryanodine receptor 2 by calmodulin.
Journal, issue, pagesNature, Vol. 572, Issue 7769, Page 347-351, Year 2019
Publish dateJul 5, 2019
AuthorsDeshun Gong / Ximin Chi / Jinhong Wei / Gewei Zhou / Gaoxingyu Huang / Lin Zhang / Ruiwu Wang / Jianlin Lei / S R Wayne Chen / Nieng Yan /
PubMed AbstractThe high-conductance intracellular calcium (Ca) channel RyR2 is essential for the coupling of excitation and contraction in cardiac muscle. Among various modulators, calmodulin (CaM) regulates RyR2 ...The high-conductance intracellular calcium (Ca) channel RyR2 is essential for the coupling of excitation and contraction in cardiac muscle. Among various modulators, calmodulin (CaM) regulates RyR2 in a Ca-dependent manner. Here we reveal the regulatory mechanism by which porcine RyR2 is modulated by human CaM through the structural determination of RyR2 under eight conditions. Apo-CaM and Ca-CaM bind to distinct but overlapping sites in an elongated cleft formed by the handle, helical and central domains. The shift in CaM-binding sites on RyR2 is controlled by Ca binding to CaM, rather than to RyR2. Ca-CaM induces rotations and intradomain shifts of individual central domains, resulting in pore closure of the PCB95 and Ca-activated channel. By contrast, the pore of the ATP, caffeine and Ca-activated channel remains open in the presence of Ca-CaM, which suggests that Ca-CaM is one of the many competing modulators of RyR2 gating.
External linksNature / PubMed:31278385
MethodsEM (single particle)
Resolution3.6 - 4.4 Å
Structure data

EMDB-9831, PDB-6ji0:
Structure of RyR2 (F/A/C/Ca2+ dataset)
Method: EM (single particle) / Resolution: 4.2 Å

EMDB-9833, PDB-6ji8:
Structure of RyR2 (F/apoCaM dataset)
Method: EM (single particle) / Resolution: 3.6 Å

EMDB-9834, PDB-6jii:
Structure of RyR2 (F/A/C/L-Ca2+/apo-CaM-M dataset)
Method: EM (single particle) / Resolution: 4.2 Å

EMDB-9836, PDB-6jiu:
Structure of RyR2 (F/A/C/L-Ca2+/Ca2+CaM dataset)
Method: EM (single particle) / Resolution: 4.2 Å

EMDB-9837, PDB-6jiy:
Structure of RyR2 (F/A/C/H-Ca2+/Ca2+CaM dataset)
Method: EM (single particle) / Resolution: 3.9 Å

EMDB-9879, PDB-6jrr:
Structure of RyR2 (*F/A/C/L-Ca2+ dataset)
Method: EM (single particle) / Resolution: 3.9 Å

EMDB-9880, PDB-6jrs:
Structure of RyR2 (*F/A/C/L-Ca2+/Ca2+-CaM dataset)
Method: EM (single particle) / Resolution: 3.7 Å

EMDB-9889, PDB-6jv2:
Structure of RyR2 (P/L-Ca2+/Ca2+-CaM dataset)
Method: EM (single particle) / Resolution: 4.4 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

ChemComp-CA:
Unknown entry

ChemComp-CFF:
CAFFEINE / medication*YM

Source
  • sus scrofa (pig)
  • homo sapiens (human)
KeywordsMEMBRANE PROTEIN / cryo-EM / MEMBRANE PROTEIN/ISOMERASE / MEMBRANE PROTEIN-ISOMERASE complex

+
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