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- PDB-2mc2: X-ray crystallography-solution NMR hybrid structure of mouse RyR2... -

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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


manganese ion transmembrane transport / suramin binding / establishment of protein localization to endoplasmic reticulum / type B pancreatic cell apoptotic process / Purkinje myocyte to ventricular cardiac muscle cell signaling / regulation of SA node cell action potential / regulation of atrial cardiac muscle cell action potential / left ventricular cardiac muscle tissue morphogenesis / organic cyclic compound binding / regulation of AV node cell action potential ...manganese ion transmembrane transport / suramin binding / establishment of protein localization to endoplasmic reticulum / type B pancreatic cell apoptotic process / Purkinje myocyte to ventricular cardiac muscle cell signaling / regulation of SA node cell action potential / regulation of atrial cardiac muscle cell action potential / left ventricular cardiac muscle tissue morphogenesis / organic cyclic compound binding / regulation of AV node cell action potential / calcium-induced calcium release activity / sarcoplasmic reticulum calcium ion transport / Stimuli-sensing channels / Ion homeostasis / ventricular cardiac muscle cell action potential / regulation of ventricular cardiac muscle cell action potential / positive regulation of sequestering of calcium ion / embryonic heart tube morphogenesis / cardiac muscle hypertrophy / ryanodine-sensitive calcium-release channel activity / response to muscle activity / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / calcium ion transport into cytosol / calcium ion transmembrane import into cytosol / response to caffeine / A band / response to redox state / positive regulation of heart rate / negative regulation of cytosolic calcium ion concentration / cellular response to caffeine / protein kinase A regulatory subunit binding / intracellularly gated calcium channel activity / protein kinase A catalytic subunit binding / positive regulation of the force of heart contraction / response to magnesium ion / : / detection of calcium ion / smooth endoplasmic reticulum / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / striated muscle contraction / monoatomic ion transmembrane transport / extrinsic component of cytoplasmic side of plasma membrane / sarcoplasmic reticulum membrane / calcium channel complex / cellular response to epinephrine stimulus / regulation of cytosolic calcium ion concentration / response to muscle stretch / regulation of heart rate / sarcomere / sarcoplasmic reticulum / establishment of localization in cell / calcium-mediated signaling / calcium ion transmembrane transport / calcium channel activity / sarcolemma / Z disc / intracellular calcium ion homeostasis / response to calcium ion / calcium ion transport / : / nuclear envelope / scaffold protein binding / 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 junctional solenoid repeat / Ryanodine receptor, SPRY domain 2 / 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 junctional solenoid repeat / Ryanodine receptor, SPRY domain 2 / 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 / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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Experimental details

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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.

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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

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NMR measurement

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

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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

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