+Open data
-Basic information
Entry | Database: PDB / ID: 2k2f | ||||||
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Title | Solution structure of Ca2+-S100A1-RyRP12 | ||||||
Components |
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Keywords | METAL BINDING PROTEIN / S100 / EF hand / ryanodine receptor / calcium binding / Alternative splicing / Calcium channel / Calcium transport / Glycoprotein / Ion transport / Ionic channel / Membrane / Polymorphism / Transmembrane / Transport / Cytoplasm / Metal-binding / Zinc | ||||||
Function / homology | Function and homology information Stimuli-sensing channels / Regulation of TLR by endogenous ligand / 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 / sarcoplasmic reticulum calcium ion transport ...Stimuli-sensing channels / Regulation of TLR by endogenous ligand / 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 / sarcoplasmic reticulum calcium ion transport / left ventricular cardiac muscle tissue morphogenesis / organic cyclic compound binding / regulation of AV node cell action potential / calcium-induced calcium release activity / regulation of ventricular cardiac muscle cell action potential / ventricular cardiac muscle cell action potential / positive regulation of sequestering of calcium ion / cardiac muscle hypertrophy / embryonic heart tube morphogenesis / regulation of cardiac muscle contraction by calcium ion signaling / S100 protein binding / M band / calcium ion transport into cytosol / ryanodine-sensitive calcium-release channel activity / response to muscle activity / I band / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / response to caffeine / A band / response to redox state / calcium ion transmembrane import into cytosol / positive regulation of heart rate / Ion homeostasis / regulation of heart contraction / negative regulation of cytosolic calcium ion concentration / positive regulation of sprouting angiogenesis / cellular response to caffeine / protein kinase A regulatory subunit binding / extrinsic component of cytoplasmic side of plasma membrane / protein kinase A catalytic subunit binding / response to magnesium ion / positive regulation of the force of heart contraction / intracellularly gated calcium channel activity / regulation of cardiac muscle contraction / detection of calcium ion / smooth endoplasmic reticulum / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / striated muscle contraction / cardiac muscle contraction / release of sequestered calcium ion into cytosol / regulation of cytosolic calcium ion concentration / sarcoplasmic reticulum membrane / calcium channel complex / cellular response to epinephrine stimulus / response to muscle stretch / sarcomere / regulation of heart rate / response to nutrient / sarcoplasmic reticulum / establishment of localization in cell / calcium ion transmembrane transport / calcium-mediated signaling / calcium channel activity / sarcolemma / Z disc / intracellular calcium ion homeostasis / response to calcium ion / calcium-dependent protein binding / calcium ion transport / monoatomic ion transmembrane transport / nuclear envelope / ATPase binding / scaffold protein binding / response to hypoxia / calmodulin binding / response to xenobiotic stimulus / calcium ion binding / protein kinase binding / negative regulation of transcription by RNA polymerase II / enzyme binding / protein homodimerization activity / protein-containing complex / mitochondrion / identical protein binding / membrane / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | SOLUTION NMR / DGSA-distance geometry simulated annealing | ||||||
Model details | calcium loaded S100A1 bound to a peptide from the calmodulin binding domain of RyR1 | ||||||
Authors | Wright, N.T. / Varney, K.M. / Weber, D.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: S100A1 and Calmodulin Compete for the Same Binding Site on Ryanodine Receptor. Authors: Wright, N.T. / Prosser, B.L. / Varney, K.M. / Zimmer, D.B. / Schneider, M.F. / Weber, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2k2f.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2k2f.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 2k2f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2k2f_validation.pdf.gz | 365.7 KB | Display | wwPDB validaton report |
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Full document | 2k2f_full_validation.pdf.gz | 776.7 KB | Display | |
Data in XML | 2k2f_validation.xml.gz | 82.3 KB | Display | |
Data in CIF | 2k2f_validation.cif.gz | 125.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k2/2k2f ftp://data.pdbj.org/pub/pdb/validation_reports/k2/2k2f | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 1470.822 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: RYR1 / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): HMS(DE3) / References: UniProt: B0LPN4*PLUS #2: Protein | Mass: 10439.614 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: S100a1 / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): HMS(DE3) / References: UniProt: P35467 #3: Chemical | ChemComp-CA / |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR Details: calcium loaded S100A1 bound to a peptide from the calmodulin binding domain of RyR1 | ||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 10-15 mM CALCIUM ION, 1-3 mM [U-100% 13C; U-100% 15N] RYR1 peptide, 2-6 mM S100-A1 protein, 10 % D2O, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | ||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 40-50 / pH: 7.2 / Pressure: ambient / Temperature: 310 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: DGSA-distance geometry simulated annealing / Software ordinal: 1 | |||||||||
NMR representative | Selection criteria: closest to the average | |||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 20 |