[English] 日本語
Yorodumi
- PDB-2mc2: X-ray crystallography-solution NMR hybrid structure of mouse RyR2... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2mc2
TitleX-ray crystallography-solution NMR hybrid structure of mouse RyR2 domain A
ComponentsRyanodine receptor 2
KeywordsMETAL TRANSPORT / ryanodine receptor / type II / alpha2 helix
Function / homology
Function and homology information


establishment of protein localization to endoplasmic reticulum / type B pancreatic cell apoptotic process / Purkinje myocyte to ventricular cardiac muscle cell signaling / regulation of atrial cardiac muscle cell action potential / left ventricular cardiac muscle tissue morphogenesis / suramin binding / regulation of AV node cell action potential / regulation of SA node cell action potential / Stimuli-sensing channels / regulation of ventricular cardiac muscle cell action potential ...establishment of protein localization to endoplasmic reticulum / type B pancreatic cell apoptotic process / Purkinje myocyte to ventricular cardiac muscle cell signaling / regulation of atrial cardiac muscle cell action potential / left ventricular cardiac muscle tissue morphogenesis / suramin binding / regulation of AV node cell action potential / regulation of SA node cell action potential / Stimuli-sensing channels / regulation of ventricular cardiac muscle cell action potential / ventricular cardiac muscle cell action potential / positive regulation of sequestering of calcium ion / embryonic heart tube morphogenesis / cardiac muscle hypertrophy / Ion homeostasis / calcium ion transport into cytosol / ryanodine-sensitive calcium-release channel activity / response to caffeine / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / response to redox state / cellular response to caffeine / calcium ion transmembrane import into cytosol / response to muscle activity / protein kinase A regulatory subunit binding / protein kinase A catalytic subunit binding / positive regulation of the force of heart contraction / intracellularly gated calcium channel activity / smooth endoplasmic reticulum / detection of calcium ion / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / positive regulation of heart rate / response to muscle stretch / calcium channel complex / cellular response to epinephrine stimulus / sarcoplasmic reticulum membrane / regulation of heart rate / sarcoplasmic reticulum / sarcomere / establishment of localization in cell / calcium-mediated signaling / calcium ion transmembrane transport / calcium channel activity / Z disc / intracellular calcium ion homeostasis / calcium ion transport / calmodulin binding / response to hypoxia / calcium ion binding / protein kinase binding / enzyme binding / protein-containing complex / identical protein binding / membrane
Similarity search - Function
Ryanodine receptor, SPRY domain 2 / : / Ryanodine receptor junctional solenoid repeat / Ryanodine Receptor TM 4-6 / Ryanodine receptor / Ryanodine receptor, SPRY domain 1 / Ryanodine receptor, SPRY domain 3 / Ryanodine Receptor TM 4-6 / Ryanodine receptor Ryr / RyR domain ...Ryanodine receptor, SPRY domain 2 / : / Ryanodine receptor junctional solenoid repeat / Ryanodine Receptor TM 4-6 / Ryanodine receptor / Ryanodine receptor, SPRY domain 1 / Ryanodine receptor, SPRY domain 3 / Ryanodine Receptor TM 4-6 / Ryanodine receptor Ryr / RyR domain / RyR/IP3 receptor binding core, RIH domain superfamily / RyR/IP3R Homology associated domain / Inositol 1,4,5-trisphosphate/ryanodine receptor / RIH domain / RyR and IP3R Homology associated / Inositol 1,4,5-trisphosphate/ryanodine receptor / RIH domain / : / MIR motif / MIR domain / MIR domain profile. / Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases / Mir domain superfamily / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / EF-hand domain pair / EF-hand domain / Ion transport domain / Ion transport protein / EF-hand domain pair / Concanavalin A-like lectin/glucanase domain superfamily / Mainly Beta
Similarity search - Domain/homology
Ryanodine receptor 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsAmador, F. / Stathopulos, P. / Seabrook, G. / Ikura, M.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Type 2 Ryanodine Receptor Domain A Contains a Unique and Dynamic alpha-Helix That Transitions to a beta-Strand in a Mutant Linked with a Heritable Cardiomyopathy.
Authors: Amador, F.J. / Kimlicka, L. / Stathopulos, P.B. / Gasmi-Seabrook, G.M. / Maclennan, D.H. / Van Petegem, F. / Ikura, M.
History
DepositionAug 13, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2013Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ryanodine receptor 2


Theoretical massNumber of molelcules
Total (without water)24,1691
Polymers24,1691
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Ryanodine receptor 2 / RYR-2 / RyR2 / Cardiac muscle ryanodine receptor / Cardiac muscle ryanodine receptor-calcium ...RYR-2 / RyR2 / Cardiac muscle ryanodine receptor / Cardiac muscle ryanodine receptor-calcium release channel / Type 2 ryanodine receptor


Mass: 24169.158 Da / Num. of mol.: 1 / Fragment: domain A (UNP residues 10-224)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ryr2 / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / References: UniProt: E9Q401
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HN(CA)CB
1413D HNCO
1513D HNCA
1613D HN(CO)CA
NMR detailsText: TROSY pulse sequences were employed.

-
Sample preparation

DetailsContents: 0.4 mM [U-13C; U-15N; U-2H] RyR2, 20 mM sodium phosphate, 300 mM sodium chloride, 2 mM TCEP, 5 mM DTT, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMRyR2-1[U-13C; U-15N; U-2H]1
20 mMsodium phosphate-21
300 mMsodium chloride-31
2 mMTCEP-41
5 mMDTT-51
Sample conditionsIonic strength: 0.328 / pH: 7 / Pressure: ambient / Temperature: 288 K

-
NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

-
Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.peak picking
TALOSCornilescu, Delaglio and Baxdata analysis
TALOSCornilescu, Delaglio and Baxgeometry optimization
TALOSCornilescu, Delaglio and Baxchemical shift calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The RECOORD scripts [Proteins. 2005 Jun 1;59(4):662-72] were employed to reanneal and refine the structure with the addition of the new NMR restraints. PDB entry 3IM5 was used as the ...Details: The RECOORD scripts [Proteins. 2005 Jun 1;59(4):662-72] were employed to reanneal and refine the structure with the addition of the new NMR restraints. PDB entry 3IM5 was used as the starting structure for refinement.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

+
About Yorodumi

-
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

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more