[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 of RyR1 in native membranes.
Journal, issue, pagesEMBO Rep, Vol. 21, Issue 5, Page e49891, Year 2020
Publish dateMay 6, 2020
AuthorsWenbo Chen / Mikhail Kudryashev /
PubMed AbstractRyanodine receptor 1 (RyR1) mediates excitation-contraction coupling by releasing Ca from sarcoplasmic reticulum (SR) to the cytoplasm of skeletal muscle cells. RyR1 activation is regulated by ...Ryanodine receptor 1 (RyR1) mediates excitation-contraction coupling by releasing Ca from sarcoplasmic reticulum (SR) to the cytoplasm of skeletal muscle cells. RyR1 activation is regulated by several proteins from both the cytoplasm and lumen of the SR. Here, we report the structure of RyR1 from native SR membranes in closed and open states. Compared to the previously reported structures of purified RyR1, our structure reveals helix-like densities traversing the bilayer approximately 5 nm from the RyR1 transmembrane domain and sarcoplasmic extensions linking RyR1 to a putative calsequestrin network. We document the primary conformation of RyR1 in situ and its structural variations. The activation of RyR1 is associated with changes in membrane curvature and movement in the sarcoplasmic extensions. Our results provide structural insight into the mechanism of RyR1 in its native environment.
External linksEMBO Rep / PubMed:32147968 / PubMed Central
MethodsEM (subtomogram averaging)
Resolution12.6 - 38.0 Å
Structure data

EMDB-10637:
Structure of ryanodine receptor 1 in apo state in native membrane
Method: EM (subtomogram averaging) / Resolution: 12.6 Å

EMDB-10638:
Structure of Ryanodine Receptor 1 in the presence of ryanodine in native membrane (with Calcium)
Method: EM (subtomogram averaging) / Resolution: 17.5 Å

EMDB-10639:
Structure of ryanodine receptor 1 in apo state in native membrane with the T-tubule membrane
Method: EM (subtomogram averaging) / Resolution: 38.0 Å

EMDB-10640:
Rabbit ryanodine receptor 1 in the presence of 1mM Calcium in native membrane
Method: EM (subtomogram averaging) / Resolution: 27.7 Å

EMDB-10641:
Structure of ryanodine receptor 1 in native membrane in the presence of DDM and EDTA
Method: EM (subtomogram averaging) / Resolution: 25.7 Å

EMDB-10642:
Structure of rabbit ryanodine receptor 1 in apo state in native membrane (class 1)
Method: EM (subtomogram averaging) / Resolution: 15.4 Å

EMDB-10643:
Structure of rabbit ryanodine receptor 1 in apo state in native membrane (class 2)
Method: EM (subtomogram averaging) / Resolution: 18.0 Å

EMDB-10644:
Structure of ryanodine receptor 1 in apo state in native membrane (class 3)
Method: EM (subtomogram averaging) / Resolution: 18.0 Å

EMDB-10645:
Structure of ryanodine receptor 1 in apo state in native membrane (class 4)
Method: EM (subtomogram averaging) / Resolution: 21.6 Å

EMDB-10646:
Structure of ryanodine receptor 1 in native membrane in the presence of 5mM Calcium
Method: EM (subtomogram averaging) / Resolution: 30.0 Å

Source
  • Oryctolagus cuniculus (rabbit)

+
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