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Yorodumi- PDB-6y4p: Calmodulin N53I variant bound to cardiac ryanodine receptor (RyR2... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6y4p | |||||||||||||||
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Title | Calmodulin N53I variant bound to cardiac ryanodine receptor (RyR2) calmodulin binding domain | |||||||||||||||
Components |
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Keywords | MEMBRANE PROTEIN / ion channel / calcium / calmodulin | |||||||||||||||
Function / homology | Function and homology information manganese ion transmembrane transport / junctional sarcoplasmic reticulum membrane / 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 ...manganese ion transmembrane transport / junctional sarcoplasmic reticulum membrane / 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 / positive regulation of ATPase-coupled calcium transmembrane transporter activity / 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 / embryonic heart tube morphogenesis / regulation of cardiac muscle contraction by calcium ion signaling / cardiac muscle hypertrophy / ryanodine-sensitive calcium-release channel activity / response to muscle activity / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / CaM pathway / calcium ion transmembrane import into cytosol / Cam-PDE 1 activation / calcium ion transport into cytosol / Sodium/Calcium exchangers / A band / response to caffeine / cell communication by electrical coupling involved in cardiac conduction / response to redox state / Calmodulin induced events / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / negative regulation of high voltage-gated calcium channel activity / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / negative regulation of calcium ion export across plasma membrane / positive regulation of heart rate / organelle localization by membrane tethering / Activation of RAC1 downstream of NMDARs / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / CLEC7A (Dectin-1) induces NFAT activation / autophagosome membrane docking / negative regulation of cytosolic calcium ion concentration / positive regulation of ryanodine-sensitive calcium-release channel activity / Negative regulation of NMDA receptor-mediated neuronal transmission / regulation of cell communication by electrical coupling involved in cardiac conduction / Unblocking of NMDA receptors, glutamate binding and activation / negative regulation of peptidyl-threonine phosphorylation / cellular response to caffeine / Synthesis of IP3 and IP4 in the cytosol / intracellularly gated calcium channel activity / Phase 0 - rapid depolarisation / protein kinase A regulatory subunit binding / protein phosphatase activator activity / RHO GTPases activate PAKs / smooth endoplasmic reticulum / protein kinase A catalytic subunit binding / positive regulation of the force of heart contraction / positive regulation of cyclic-nucleotide phosphodiesterase activity / response to magnesium ion / positive regulation of phosphoprotein phosphatase activity / Long-term potentiation / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / : / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / catalytic complex / DARPP-32 events / detection of calcium ion / striated muscle contraction / negative regulation of ryanodine-sensitive calcium-release channel activity / Smooth Muscle Contraction / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction / calcium channel inhibitor activity / cellular response to interferon-beta / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Protein methylation / voltage-gated potassium channel complex / Activation of AMPK downstream of NMDARs / eNOS activation / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / regulation of calcium-mediated signaling / release of sequestered calcium ion into cytosol / positive regulation of protein dephosphorylation / titin binding / regulation of ryanodine-sensitive calcium-release channel activity / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / cardiac muscle contraction Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13325578805 Å | |||||||||||||||
Authors | Lau, K. / Nielsen, L.H. / Holt, C. / Brohus, M. / Sorensen, A.B. / Larsen, K.T. / Sommer, C. / Van Petegem, F. / Overgaard, M.T. / Wimmer, R. | |||||||||||||||
Funding support | Denmark, Germany, Canada, 4items
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Citation | Journal: J.Biol.Chem. / Year: 2020 Title: The arrhythmogenic N53I variant subtly changes the structure and dynamics in the calmodulin N-terminal domain, altering its interaction with the cardiac ryanodine receptor. Authors: Holt, C. / Hamborg, L. / Lau, K. / Brohus, M. / Sorensen, A.B. / Larsen, K.T. / Sommer, C. / Van Petegem, F. / Overgaard, M.T. / Wimmer, R. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6y4p.cif.gz | 57.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6y4p.ent.gz | 32.2 KB | Display | PDB format |
PDBx/mmJSON format | 6y4p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y4/6y4p ftp://data.pdbj.org/pub/pdb/validation_reports/y4/6y4p | HTTPS FTP |
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-Related structure data
Related structure data | 6y4oC 6y94C 6y95C 2bcxS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16851.600 Da / Num. of mol.: 1 / Mutation: N53I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CALM1, CALM, CAM, CAM1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DP23 | ||||
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#2: Protein/peptide | Mass: 3478.235 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ryr2 / Production host: Escherichia coli (E. coli) / References: UniProt: E9Q401, UniProt: Q92736*PLUS | ||||
#3: Chemical | ChemComp-CA / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Sodium Acetate pH 4.70 and 23 % PEG 550 MME |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Dec 11, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.133→45.18 Å / Num. obs: 8489 / % possible obs: 99.76 % / Redundancy: 5.9 % / Biso Wilson estimate: 24.3986621334 Å2 / CC1/2: 0.993 / Net I/σ(I): 9.45 |
Reflection shell | Resolution: 2.133→2.209 Å / Num. unique obs: 831 / CC1/2: 0.946 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2bcx Resolution: 2.13325578805→45.1799 Å / SU ML: 0.232891903909 / Cross valid method: FREE R-VALUE / σ(F): 1.43770529883 / Phase error: 21.642731085
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.4527987444 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.13325578805→45.1799 Å
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Refine LS restraints |
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LS refinement shell |
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