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Yorodumi- PDB-7vmn: Structure of recombinant RyR2 (EGTA dataset, class 2, closed state) -
+Open data
-Basic information
Entry | Database: PDB / ID: 7vmn | |||||||||||||||||||||
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Title | Structure of recombinant RyR2 (EGTA dataset, class 2, closed state) | |||||||||||||||||||||
Components |
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Keywords | MEMBRANE 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 / 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 / cyclic nucleotide binding / embryonic heart tube morphogenesis / negative regulation of release of sequestered calcium ion into cytosol / negative regulation of insulin secretion involved in cellular response to glucose stimulus / regulation of cardiac muscle contraction by calcium ion signaling / cardiac muscle hypertrophy / ryanodine-sensitive calcium-release channel activity / neuronal action potential propagation / insulin secretion involved in cellular response to glucose stimulus / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / response to muscle activity / calcium ion transmembrane import into cytosol / calcium ion transport into cytosol / A band / response to caffeine / cell communication by electrical coupling involved in cardiac conduction / response to redox state / protein maturation by protein folding / 'de novo' protein folding / negative regulation of heart rate / negative regulation of phosphoprotein phosphatase activity / FK506 binding / positive regulation of heart rate / negative regulation of cytosolic calcium ion concentration / positive regulation of axon regeneration / cellular response to caffeine / protein kinase A regulatory subunit binding / intracellularly gated calcium channel activity / smooth endoplasmic reticulum / protein kinase A catalytic subunit binding / positive regulation of the force of heart contraction / response to magnesium ion / : / detection of calcium ion / smooth muscle contraction / striated muscle contraction / negative regulation of ryanodine-sensitive calcium-release channel activity / response to vitamin E / regulation of cardiac muscle contraction / calcium channel inhibitor activity / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / protein peptidyl-prolyl isomerization / T cell proliferation / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / release of sequestered calcium ion into cytosol / Ion homeostasis / regulation of ryanodine-sensitive calcium-release channel activity / cardiac muscle contraction / sarcoplasmic reticulum membrane / calcium channel complex / cellular response to epinephrine stimulus / regulation of cytosolic calcium ion concentration / response to muscle stretch / extrinsic component of cytoplasmic side of plasma membrane / regulation of heart rate / sarcomere / monoatomic ion transmembrane transport / sarcoplasmic reticulum / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / establishment of localization in cell / calcium-mediated signaling / calcium ion transmembrane transport / sarcolemma / response to hydrogen peroxide / calcium channel activity / Stimuli-sensing channels / intracellular calcium ion homeostasis / Z disc / response to calcium ion / : / calcium ion transport / nuclear envelope / positive regulation of cytosolic calcium ion concentration / protein refolding / scaffold protein binding / transmembrane transporter binding / response to hypoxia / calmodulin binding / signaling receptor binding / calcium ion binding / protein kinase binding / enzyme binding Similarity search - Function | |||||||||||||||||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||||||||||||||
Authors | Kobayashi, T. / Tsutsumi, A. / Kurebayashi, N. / Kodama, M. / Kikkawa, M. / Murayama, T. / Ogawa, H. | |||||||||||||||||||||
Funding support | Japan, 6items
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Citation | Journal: Nat Commun / Year: 2022 Title: Molecular basis for gating of cardiac ryanodine receptor explains the mechanisms for gain- and loss-of function mutations. Authors: Takuya Kobayashi / Akihisa Tsutsumi / Nagomi Kurebayashi / Kei Saito / Masami Kodama / Takashi Sakurai / Masahide Kikkawa / Takashi Murayama / Haruo Ogawa / Abstract: Cardiac ryanodine receptor (RyR2) is a large Ca release channel in the sarcoplasmic reticulum and indispensable for excitation-contraction coupling in the heart. RyR2 is activated by Ca and RyR2 ...Cardiac ryanodine receptor (RyR2) is a large Ca release channel in the sarcoplasmic reticulum and indispensable for excitation-contraction coupling in the heart. RyR2 is activated by Ca and RyR2 mutations are implicated in severe arrhythmogenic diseases. Yet, the structural basis underlying channel opening and how mutations affect the channel remains unknown. Here, we address the gating mechanism of RyR2 by combining high-resolution structures determined by cryo-electron microscopy with quantitative functional analysis of channels carrying various mutations in specific residues. We demonstrated two fundamental mechanisms for channel gating: interactions close to the channel pore stabilize the channel to prevent hyperactivity and a series of interactions in the surrounding regions is necessary for channel opening upon Ca binding. Mutations at the residues involved in the former and the latter mechanisms cause gain-of-function and loss-of-function, respectively. Our results reveal gating mechanisms of the RyR2 channel and alterations by pathogenic mutations at the atomic level. | |||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vmn.cif.gz | 2.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7vmn.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7vmn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vm/7vmn ftp://data.pdbj.org/pub/pdb/validation_reports/vm/7vmn | HTTPS FTP |
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-Related structure data
Related structure data | 33937MC 7vmlC 7vmmC 7vmoC 7vmpC 7vmrC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 533653.562 Da / Num. of mol.: 4 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 | 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 / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Recombinant RyR2 in the presence of EGTA / Type: CELL / Details: in complex with FKBP12.6 / Entity ID: #1-#2 / Source: RECOMBINANT |
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Source (natural) | Organism: Mus musculus (house mouse) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
EM embedding | Material: buffer |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 41197 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Refine LS restraints |
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