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- PDB-7vms: Structure of recombinant RyR2 mutant K4593A (Ca2+ dataset) -

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Basic information

Entry
Database: PDB / ID: 7vms
TitleStructure of recombinant RyR2 mutant K4593A (Ca2+ dataset)
Components
  • Peptidyl-prolyl cis-trans isomerase FKBP1B
  • Ryanodine receptor 2
KeywordsMEMBRANE PROTEIN / CALCIUM / CALCIUM CHANNEL / CALCIUM TRANSPORT / ION TRANSPORT / IONIC CHANNEL / METAL TRANSPORT / ER/SR MEMBRANE / RYANODINE RECEPTOR / RYANODINE / RECEPTOR / WILD TYPE
Function / homology
Function and homology information


manganese ion transmembrane transport / establishment of protein localization to endoplasmic reticulum / type B pancreatic cell apoptotic process / Purkinje myocyte to ventricular cardiac muscle cell signaling / suramin binding / 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 / establishment of protein localization to endoplasmic reticulum / type B pancreatic cell apoptotic process / Purkinje myocyte to ventricular cardiac muscle cell signaling / suramin binding / 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 / regulation of ventricular cardiac muscle cell action potential / ventricular cardiac muscle cell action potential / positive regulation of sequestering of calcium ion / cyclic nucleotide binding / negative regulation of calcium-mediated signaling / embryonic heart tube morphogenesis / cardiac muscle hypertrophy / negative regulation of insulin secretion involved in cellular response to glucose stimulus / negative regulation of release of sequestered calcium ion into cytosol / neuronal action potential propagation / insulin secretion involved in cellular response to glucose stimulus / ryanodine-sensitive calcium-release channel activity / response to caffeine / calcium ion transport into cytosol / response to muscle activity / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / A band / response to redox state / protein maturation by protein folding / calcium ion transmembrane import into cytosol / 'de novo' protein folding / negative regulation of heart rate / positive regulation of heart rate / FK506 binding / negative regulation of cytosolic calcium ion concentration / positive regulation of axon regeneration / protein kinase A regulatory subunit binding / cellular response to caffeine / extrinsic component of cytoplasmic side of plasma membrane / protein kinase A catalytic subunit binding / channel regulator activity / positive regulation of the force of heart contraction / intracellularly gated calcium channel activity / response to magnesium ion / detection of calcium ion / smooth muscle contraction / response to vitamin E / smooth endoplasmic reticulum / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium channel inhibitor activity / striated muscle contraction / T cell proliferation / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Ion homeostasis / release of sequestered calcium ion into cytosol / regulation of cytosolic calcium ion concentration / calcium channel complex / cellular response to epinephrine stimulus / response to muscle stretch / sarcoplasmic reticulum membrane / regulation of heart rate / sarcomere / sarcoplasmic reticulum / establishment of localization in cell / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / calcium-mediated signaling / calcium ion transmembrane transport / calcium channel activity / response to hydrogen peroxide / sarcolemma / Stimuli-sensing channels / Z disc / response to calcium ion / intracellular calcium ion homeostasis / calcium ion transport / nuclear envelope / positive regulation of cytosolic calcium ion concentration / protein refolding / monoatomic ion transmembrane transport / scaffold protein binding / transmembrane transporter binding / calmodulin binding / response to hypoxia / signaling receptor binding / calcium ion binding / protein kinase binding / enzyme binding / protein-containing complex / identical protein binding / membrane / cytosol / cytoplasm
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 / 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 / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily / EF-hand domain pair / EF-hand domain / Ion transport domain / Ion transport protein / EF-hand domain pair / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Ryanodine receptor 2 / Peptidyl-prolyl cis-trans isomerase FKBP1B
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsKobayashi, T. / Tsutsumi, A. / Kurebayashi, N. / Kodama, M. / Kikkawa, M. / Murayama, T. / Ogawa, H.
Funding support Japan, 6items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP16H04748 Japan
Japan Society for the Promotion of Science (JSPS)JP19K07105 Japan
Japan Society for the Promotion of Science (JSPS)19H03404 Japan
Japan Society for the Promotion of Science (JSPS)JP21H02411 Japan
Japan Agency for Medical Research and Development (AMED)JP21am0101080 Japan
Japan Agency for Medical Research and Development (AMED)19ek0109202 Japan
CitationJournal: Nat Commun / Year: 2022
Title: Molecular basis for gating of cardiac ryanodine receptor explains the mechanisms for gain- and loss-of function mutations
Authors: Kobayashi, T. / Tsutsumi, A. / Kurebayashi, N. / Saito, K. / Kodama, M. / Sakurai, T. / Kikkawa, M. / Murayama, T. / Ogawa, H.
History
DepositionOct 9, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ryanodine receptor 2
G: Peptidyl-prolyl cis-trans isomerase FKBP1B
B: Ryanodine receptor 2
H: Peptidyl-prolyl cis-trans isomerase FKBP1B
C: Ryanodine receptor 2
I: Peptidyl-prolyl cis-trans isomerase FKBP1B
D: Ryanodine receptor 2
J: Peptidyl-prolyl cis-trans isomerase FKBP1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,210,74116
Polymers2,210,3198
Non-polymers4228
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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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: 533595.438 Da / Num. of mol.: 4 / Mutation: K4593A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ryr2 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: E9Q401
#2: Protein
Peptidyl-prolyl cis-trans isomerase FKBP1B / FK506-binding protein 1B / FKBP-1B /


Mass: 18984.316 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FKBP1B / Production host: Escherichia coli (E. coli) / References: UniProt: P68106, peptidylprolyl isomerase
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Recombinant RyR2 mutant K4593A in the presence of Ca2+
Type: CELL / Details: in complex with FKBP12.6 / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
EM embeddingMaterial: buffer
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 10879 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003125860
ELECTRON MICROSCOPYf_angle_d0.645170648
ELECTRON MICROSCOPYf_dihedral_angle_d13.33244016
ELECTRON MICROSCOPYf_chiral_restr0.0419404
ELECTRON MICROSCOPYf_plane_restr0.00422256

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