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Yorodumi- PDB-4j9z: Calcium-calmodulin complexed with the calmodulin binding domain f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4j9z | ||||||
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Title | Calcium-calmodulin complexed with the calmodulin binding domain from a small conductance potassium channel splice variant and NS309 | ||||||
Components |
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Keywords | TRANSPORT PROTEIN/CALCIUM BINDING / Calcium binding / EF hand / SK2a channel fragment / TRANSPORT PROTEIN-CALCIUM BINDING complex | ||||||
Function / homology | Function and homology information Ca2+ activated K+ channels / small conductance calcium-activated potassium channel activity / regulation of store-operated calcium channel activity / membrane repolarization during atrial cardiac muscle cell action potential / regulation of high voltage-gated calcium channel activity / calcium-activated potassium channel activity / : / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex ...Ca2+ activated K+ channels / small conductance calcium-activated potassium channel activity / regulation of store-operated calcium channel activity / membrane repolarization during atrial cardiac muscle cell action potential / regulation of high voltage-gated calcium channel activity / calcium-activated potassium channel activity / : / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / : / establishment of protein localization to mitochondrial membrane / positive regulation of potassium ion transport / inward rectifier potassium channel activity / type 3 metabotropic glutamate receptor binding / regulation of potassium ion transmembrane transport / establishment of protein localization to membrane / regulation of synaptic vesicle endocytosis / negative regulation of high voltage-gated calcium channel activity / positive regulation of cyclic-nucleotide phosphodiesterase activity / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / regulation of synaptic vesicle exocytosis / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / nitric-oxide synthase binding / positive regulation of ryanodine-sensitive calcium-release channel activity / alpha-actinin binding / regulation of neuronal synaptic plasticity / protein phosphatase activator activity / positive regulation of phosphoprotein phosphatase activity / adenylate cyclase binding / catalytic complex / calcium channel regulator activity / detection of calcium ion / regulation of cardiac muscle contraction / smooth endoplasmic reticulum / negative regulation of ryanodine-sensitive calcium-release channel activity / calcium channel inhibitor activity / cellular response to interferon-beta / positive regulation of DNA binding / phosphatidylinositol 3-kinase binding / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / enzyme regulator activity / positive regulation of protein dephosphorylation / regulation of calcium-mediated signaling / regulation of ryanodine-sensitive calcium-release channel activity / titin binding / potassium ion transmembrane transport / voltage-gated potassium channel complex / sperm midpiece / T-tubule / calcium channel complex / response to amphetamine / activation of adenylate cyclase activity / adenylate cyclase activator activity / nitric-oxide synthase regulator activity / regulation of heart rate / sarcomere / protein serine/threonine kinase activator activity / regulation of cytokinesis / positive regulation of nitric-oxide synthase activity / calcium-mediated signaling / positive regulation of receptor signaling pathway via JAK-STAT / potassium ion transport / modulation of chemical synaptic transmission / spindle microtubule / sarcolemma / Z disc / cellular response to type II interferon / spindle pole / response to calcium ion / G2/M transition of mitotic cell cycle / calcium-dependent protein binding / disordered domain specific binding / myelin sheath / growth cone / postsynaptic membrane / vesicle / transmembrane transporter binding / protein autophosphorylation / dendritic spine / calmodulin binding / neuron projection / positive regulation of apoptotic process / protein domain specific binding / centrosome / neuronal cell body / glutamatergic synapse / calcium ion binding / protein kinase binding / cell surface / protein homodimerization activity / protein-containing complex / mitochondrion / nucleoplasm / membrane / nucleus / plasma membrane Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å | ||||||
Authors | Zhang, M. / Pascal, J.M. / Zhang, J.-F. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 Title: Unstructured to structured transition of an intrinsically disordered protein peptide in coupling Ca2+-sensing and SK channel activation. Authors: Zhang, M. / Pascal, J.M. / Zhang, J.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4j9z.cif.gz | 126.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4j9z.ent.gz | 99 KB | Display | PDB format |
PDBx/mmJSON format | 4j9z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4j9z_validation.pdf.gz | 470.5 KB | Display | wwPDB validaton report |
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Full document | 4j9z_full_validation.pdf.gz | 477.8 KB | Display | |
Data in XML | 4j9z_validation.xml.gz | 14.3 KB | Display | |
Data in CIF | 4j9z_validation.cif.gz | 20 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j9/4j9z ftp://data.pdbj.org/pub/pdb/validation_reports/j9/4j9z | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules BR
#1: Protein | Mass: 12243.395 Da / Num. of mol.: 1 / Fragment: Calmodulin Binding Domain (UNP residues 396-487) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Kcnn2 / Production host: Escherichia coli (E. coli) / References: UniProt: P70604 |
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#2: Protein | Mass: 16852.545 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) Gene: Calm1, Calm, Cam, Cam1, Calm2, Cam2, Camb, Calm3, Cam3, Camc Production host: Escherichia coli (E. coli) / References: UniProt: P62161, UniProt: P0DP29*PLUS |
-Non-polymers , 5 types, 164 molecules
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-1KP / ( | #5: Chemical | #6: Chemical | ChemComp-GOL / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.12 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 1.25 M lithium sulfate, 0.5 M ammonium sulfate, 0.1 M sodium citrate, pH 5.6, vapor diffusion, hanging drop, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.0781 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 24, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) channel cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0781 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.66→27.79 Å / Num. all: 38789 / Num. obs: 38789 / % possible obs: 99.6 % / Redundancy: 5.2 % / Rsym value: 0.052 / Net I/σ(I): 17.7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.66→27.79 Å / Occupancy max: 1 / Occupancy min: 0.29 / FOM work R set: 0.8381 / SU ML: 0.17 / σ(F): 1.36 / Phase error: 23.48 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 150.18 Å2 / Biso mean: 40.7742 Å2 / Biso min: 16.29 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.66→27.79 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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