[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

TitlePathological conformations of disease mutant Ryanodine Receptors revealed by cryo-EM.
Journal, issue, pagesNat Commun, Vol. 12, Issue 1, Page 807, Year 2021
Publish dateFeb 5, 2021
AuthorsKellie A Woll / Omid Haji-Ghassemi / Filip Van Petegem /
PubMed AbstractRyanodine Receptors (RyRs) are massive channels that release Ca from the endoplasmic and sarcoplasmic reticulum. Hundreds of mutations are linked to malignant hyperthermia (MH), myopathies, and ...Ryanodine Receptors (RyRs) are massive channels that release Ca from the endoplasmic and sarcoplasmic reticulum. Hundreds of mutations are linked to malignant hyperthermia (MH), myopathies, and arrhythmias. Here, we explore the first MH mutation identified in humans by providing cryo-EM snapshots of the pig homolog, R615C, showing that it affects an interface between three solenoid regions. We also show the impact of apo-calmodulin (apoCaM) and how it can induce opening by bending of the bridging solenoid, mediated by its N-terminal lobe. For R615C RyR1, apoCaM binding abolishes a pathological 'intermediate' conformation, distributing the population to a mixture of open and closed channels, both different from the structure without apoCaM. Comparisons show that the mutation primarily affects the closed state, inducing partial movements linked to channel activation. This shows that disease mutations can cause distinct pathological conformations of the RyR and facilitate channel opening by disrupting interactions between different solenoid regions.
External linksNat Commun / PubMed:33547325 / PubMed Central
MethodsEM (single particle)
Resolution3.8 - 4.7 Å
Structure data

21513

6w1n

EMDB-21513, PDB-6w1n:
Pig Ryanodine Receptor (WT) in 5mM EGTA condition
Method: EM (single particle) / Resolution: 4.0 Å

22015

6x32

EMDB-22015, PDB-6x32:
Wt pig RyR1 in complex with apoCaM, EGTA condition (class 1 and 2, closed)
Method: EM (single particle) / Resolution: 3.8 Å

22016

6x33

EMDB-22016, PDB-6x33:
Wt pig RyR1 in complex with apoCaM, EGTA condition (class 3, open)
Method: EM (single particle) / Resolution: 4.2 Å

22017

6x34

EMDB-22017, PDB-6x34:
Pig R615C RyR1 EGTA (all classes, open)
Method: EM (single particle) / Resolution: 4.7 Å

22018

6x35

EMDB-22018, PDB-6x35:
Pig R615C RyR1 in complex with CaM, EGTA (class 1, open)
Method: EM (single particle) / Resolution: 4.2 Å

22019

6x36

EMDB-22019, PDB-6x36:
Pig R615C RyR1 in complex with CaM, EGTA (class 3, closed)
Method: EM (single particle) / Resolution: 4.7 Å

Chemicals

ChemComp-ZN:
Unknown entry

Source
  • sus scrofa (pig)
  • homo sapiens (human)
KeywordsTRANSPORT PROTEIN/ISOMERASE / receptor / calcium / channel / complex / TRANSPORT PROTEIN-ISOMERASE complex / TRANSPORT PROTEIN/ISOMERASE/CALCIUM BINDING PROTEIN / TRANSPORT PROTEIN-ISOMERASE-CALCIUM BINDING PROTEIN 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