[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

TitleAllosteric modulation of ryanodine receptor RyR1 by nucleotide derivatives.
Journal, issue, pagesStructure, Vol. 31, Issue 7, Page 790-800.e4, Year 2023
Publish dateJul 6, 2023
AuthorsSpencer Cholak / James W Saville / Xing Zhu / Alison M Berezuk / Katharine S Tuttle / Omid Haji-Ghassemi / Francisco J Alvarado / Filip Van Petegem / Sriram Subramaniam /
PubMed AbstractThe coordinated release of Ca from the sarcoplasmic reticulum (SR) is critical for excitation-contraction coupling. This release is facilitated by ryanodine receptors (RyRs) that are embedded in the ...The coordinated release of Ca from the sarcoplasmic reticulum (SR) is critical for excitation-contraction coupling. This release is facilitated by ryanodine receptors (RyRs) that are embedded in the SR membrane. In skeletal muscle, activity of RyR1 is regulated by metabolites such as ATP, which upon binding increase channel open probability (P). To obtain structural insights into the mechanism of RyR1 priming by ATP, we determined several cryo-EM structures of RyR1 bound individually to ATP-γ-S, ADP, AMP, adenosine, adenine, and cAMP. We demonstrate that adenine and adenosine bind RyR1, but AMP is the smallest ATP derivative capable of inducing long-range (>170 Å) structural rearrangements associated with channel activation, establishing a structural basis for key binding site interactions that are the threshold for triggering quaternary structural changes. Our finding that cAMP also induces these structural changes and results in increased channel opening suggests its potential role as an endogenous modulator of RyR1 conductance.
External linksStructure / PubMed:37192614 / PubMed Central
MethodsEM (single particle)
Resolution2.84 - 3.98 Å
Structure data

40422

8sen

EMDB-40422, PDB-8sen:
Cryo-EM Structure of RyR1
Method: EM (single particle) / Resolution: 3.49 Å

40423

8seo

EMDB-40423, PDB-8seo:
Cryo-EM Structure of RyR1 + ATP-gamma-S
Method: EM (single particle) / Resolution: 3.92 Å

40424

8sep

EMDB-40424, PDB-8sep:
Cryo-EM Structure of RyR1 + ADP
Method: EM (single particle) / Resolution: 3.57 Å

40425

8seq

EMDB-40425, PDB-8seq:
Cryo-EM Structure of RyR1 + AMP
Method: EM (single particle) / Resolution: 3.4 Å

40426

8ser

EMDB-40426, PDB-8ser:
Cryo-EM Structure of RyR1 + Adenosine
Method: EM (single particle) / Resolution: 3.42 Å

40427

8ses

EMDB-40427, PDB-8ses:
Cryo-EM Structure of RyR1 + Adenine
Method: EM (single particle) / Resolution: 3.98 Å

40428

8set

EMDB-40428, PDB-8set:
Cryo-EM Structure of RyR1 + cAMP
Method: EM (single particle) / Resolution: 3.42 Å

40429

8seu

EMDB-40429, PDB-8seu:
Cryo-EM Structure of RyR1 (Local Refinement of TMD)
Method: EM (single particle) / Resolution: 3.0 Å

40430

8sev

EMDB-40430, PDB-8sev:
Cryo-EM Structure of RyR1 + ATP-gamma-S (Local Refinement of TMD)
Method: EM (single particle) / Resolution: 3.17 Å

40431

8sew

EMDB-40431, PDB-8sew:
Cryo-EM Structure of RyR1 + ADP (Local Refinement of TMD)
Method: EM (single particle) / Resolution: 2.89 Å

40432

8sex

EMDB-40432, PDB-8sex:
Cryo-EM Structure of RyR1 + AMP (Local Refinement of TMD)
Method: EM (single particle) / Resolution: 2.84 Å

40433

8sey

EMDB-40433, PDB-8sey:
Cryo-EM Structure of RyR1 + Adenosine (Local Refinement of TMD)
Method: EM (single particle) / Resolution: 2.99 Å

40434

8sez

EMDB-40434, PDB-8sez:
Cryo-EM Structure of RyR1 + Adenine (Local Refinement of TMD)
Method: EM (single particle) / Resolution: 3.54 Å

40435

8sf0

EMDB-40435, PDB-8sf0:
Cryo-EM Structure of RyR1 + cAMP (Local Refinement of TMD)
Method: EM (single particle) / Resolution: 2.9 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

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

ChemComp-AMP:
ADENOSINE MONOPHOSPHATE / AMP*YM / Adenosine monophosphate

ChemComp-ADN:
ADENOSINE / Adenosine

ChemComp-ADE:
ADENINE / Adenine

ChemComp-CMP:
ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / Cyclic adenosine monophosphate

Source
  • oryctolagus cuniculus (rabbit)
  • rabbit (rabbit)
  • homo sapiens (human)
KeywordsTRANSPORT PROTEIN / Calcium ion channel / skeletal muscle / nucleotide / homotetramer

+
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