- PDB-5vlo: The structure of human CamKII with bound inhibitor -
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Basic information
Entry
Database: PDB / ID: 5vlo
Title
The structure of human CamKII with bound inhibitor
Components
Calcium/calmodulin-dependent protein kinase type II subunit delta
Keywords
TRANSFERASE / Kinase / CamKII / inhibitor
Function / homology
Function and homology information
regulation of relaxation of cardiac muscle / regulation of cellular localization / negative regulation of sodium ion transmembrane transport / regulation of cardiac muscle cell action potential involved in regulation of contraction / regulation of cell communication by electrical coupling / calcium- and calmodulin-dependent protein kinase complex / negative regulation of sodium ion transmembrane transporter activity / Ca2+/calmodulin-dependent protein kinase / regulation of membrane depolarization / regulation of the force of heart contraction ...regulation of relaxation of cardiac muscle / regulation of cellular localization / negative regulation of sodium ion transmembrane transport / regulation of cardiac muscle cell action potential involved in regulation of contraction / regulation of cell communication by electrical coupling / calcium- and calmodulin-dependent protein kinase complex / negative regulation of sodium ion transmembrane transporter activity / Ca2+/calmodulin-dependent protein kinase / regulation of membrane depolarization / regulation of the force of heart contraction / Trafficking of AMPA receptors / cardiac muscle cell contraction / endoplasmic reticulum calcium ion homeostasis / Assembly and cell surface presentation of NMDA receptors / sodium channel inhibitor activity / relaxation of cardiac muscle / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / calcium/calmodulin-dependent protein kinase activity / CaMK IV-mediated phosphorylation of CREB / regulation of heart contraction / regulation of cardiac muscle cell action potential / positive regulation of cardiac muscle hypertrophy / positive regulation of cardiac muscle cell apoptotic process / regulation of cell communication by electrical coupling involved in cardiac conduction / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / Phase 0 - rapid depolarisation / regulation of heart rate by cardiac conduction / Ion transport by P-type ATPases / Long-term potentiation / Regulation of MECP2 expression and activity / HSF1-dependent transactivation / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Ion homeostasis / regulation of ryanodine-sensitive calcium-release channel activity / titin binding / sarcoplasmic reticulum membrane / cellular response to calcium ion / Ras activation upon Ca2+ influx through NMDA receptor / regulation of cell growth / peptidyl-threonine phosphorylation / RAF activation / sarcolemma / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / endocytic vesicle membrane / Interferon gamma signaling / Signaling by BRAF and RAF1 fusions / RAF/MAP kinase cascade / peptidyl-serine phosphorylation / transmembrane transporter binding / protein autophosphorylation / calmodulin binding / neuron projection / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / regulation of transcription by RNA polymerase II / protein homodimerization activity / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus / cytoplasm / cytosol Similarity search - Function
Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / NTF2-like domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain ...Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / NTF2-like domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta Similarity search - Domain/homology
Chem-9EJ / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / Calcium/calmodulin-dependent protein kinase type II subunit delta Similarity search - Component
A: Calcium/calmodulin-dependent protein kinase type II subunit delta B: Calcium/calmodulin-dependent protein kinase type II subunit delta hetero molecules
Mass: 18.015 Da / Num. of mol.: 349 / Source method: isolated from a natural source / Formula: H2O
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.35 Å3/Da / Density % sol: 47.64 %
Crystal grow
Temperature: 293 K / Method: vapor diffusion, sitting drop Details: CamKII S3-K301, in 20mM imidazole pH 8.5, 0.3M sodium chloride, 5mM TCEP, was concentrated to 36 mg/ml and flash frozen in liquid nitrogen for long term storage at -80 C in 10 uL aliquots. ...Details: CamKII S3-K301, in 20mM imidazole pH 8.5, 0.3M sodium chloride, 5mM TCEP, was concentrated to 36 mg/ml and flash frozen in liquid nitrogen for long term storage at -80 C in 10 uL aliquots. The protein was thawed and diluted down to 12 mg/mL in the same buffer just prior to crystallization experiments. Sitting drop vapor diffusion droplets were assembled with 250 nL of 12 mg/mL CamKII, 0.6 mM inhibitor and 250 nL of reservoir solution 24% peg 3350, 0.2 M ammonium tartrate, 0.1 M arginine. Flat crystal plates (typically 0.03 mm x 0.2 mm x 0.4 mm in size) grew in 4-7 days at 20 C. A crystal seed suspension was prepared with ten crushed crystals combined into 100 uL of reservoir solution and stored at -80 C. A thirty fold seed dilution was prepared in the same solution for addition to protein droplets in a 1 to 1 volume ratio to enhance crystallization of difficult to crystallize inhibitors.
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Data collection
Diffraction
Mean temperature: 100 K
Diffraction source
Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
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