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Yorodumi- PDB-8dtz: Recombinant mouse RyR2 triple phosphonull mutant S2807A/S2813A/S2... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8dtz | ||||||||||||||||||
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Title | Recombinant mouse RyR2 triple phosphonull mutant S2807A/S2813A/S2030A in complex with FKBP12.6 and nanodisc under closed-state conditions | ||||||||||||||||||
Components |
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Keywords | MEMBRANE PROTEIN / Ryanodine receptor / Calcium channel / Mutation / Triple mutant / RyR2 / Phosphorylation | ||||||||||||||||||
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 / negative regulation of calcium-mediated signaling / embryonic heart tube morphogenesis / negative regulation of insulin secretion involved in cellular response to glucose stimulus / cardiac muscle hypertrophy / negative regulation of release of sequestered calcium ion into cytosol / 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 transport into cytosol / response to caffeine / 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 / cellular response to caffeine / protein kinase A regulatory subunit binding / channel regulator activity / intracellularly gated calcium channel activity / protein kinase A catalytic subunit binding / positive regulation of the force of heart contraction / extrinsic component of cytoplasmic side of plasma membrane / response to magnesium ion / detection of calcium ion / smooth muscle contraction / smooth endoplasmic reticulum / response to vitamin E / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium channel inhibitor activity / striated muscle contraction / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / T cell proliferation / release of sequestered calcium ion into cytosol / Ion homeostasis / monoatomic ion transmembrane transport / regulation of cytosolic calcium ion concentration / sarcoplasmic reticulum membrane / calcium channel complex / cellular response to epinephrine stimulus / response to muscle stretch / regulation of heart rate / sarcomere / sarcoplasmic reticulum / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / establishment of localization in cell / calcium ion transmembrane transport / calcium-mediated signaling / response to calcium ion / response to hydrogen peroxide / calcium channel activity / Stimuli-sensing channels / sarcolemma / Z disc / intracellular calcium ion homeostasis / nuclear envelope / calcium ion transport / positive regulation of cytosolic calcium ion concentration / protein refolding / 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 / cytoplasm / cytosol Similarity search - Function | ||||||||||||||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||||||||||||||
Authors | Iyer, K.A. / Hu, Y. / Murayama, T. / Samso, M. | ||||||||||||||||||
Funding support | United States, 5items
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Citation | Journal: To Be Published Title: Recombinant mouse RyR2 triple phosphonull mutant S2807A/S2813A/S2030A in complex with FKBP12.6 and nanodisc under closed-state conditions Authors: Hu, Y. / Iyer, K.A. / Nayak, A.R. / Eltit, J.M. / Kurebayashi, N. / Murayama, T. / Samso, M. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8dtz.cif.gz | 2.8 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8dtz.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8dtz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8dtz_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8dtz_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8dtz_validation.xml.gz | 393.8 KB | Display | |
Data in CIF | 8dtz_validation.cif.gz | 606.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dt/8dtz ftp://data.pdbj.org/pub/pdb/validation_reports/dt/8dtz | HTTPS FTP |
-Related structure data
Related structure data | 27712MC 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: 565488.062 Da / Num. of mol.: 4 / Mutation: S2807A, S2813A, S2030A 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: 11667.305 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FKBP1B, FKBP12.6, FKBP1L, FKBP9, OTK4 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P68106, peptidylprolyl isomerase #3: Chemical | ChemComp-ZN / Has ligand of interest | N | |
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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 mouse RyR2 triple phosphonull mutant S2807A/S2813A/S2030A in complex with FKBP12.6 and nanodisc under closed-state conditions Type: COMPLEX / Entity ID: #1-#2 / Source: MULTIPLE SOURCES | |||||||||||||||||||||||||
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Molecular weight | Value: 2.26 MDa / Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: Mus musculus (house mouse) | |||||||||||||||||||||||||
Source (recombinant) | Organism: Homo sapiens (human) | |||||||||||||||||||||||||
Buffer solution | pH: 7.4 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K |
-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 FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 1000 nm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 4.16 sec. / Electron dose: 52.95 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 5557 |
EM imaging optics | Energyfilter slit width: 20 eV |
-Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1589163 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C4 (4 fold cyclic) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 136874 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT | ||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6WOU Accession code: 6WOU / Source name: PDB / Type: experimental model |