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- PDB-2vn9: Crystal Structure of Human Calcium Calmodulin dependent Protein K... -
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Basic information
Entry | Database: PDB / ID: 2vn9 | ||||||
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Title | Crystal Structure of Human Calcium Calmodulin dependent Protein Kinase II delta isoform 1, CAMKD | ||||||
![]() | CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II DELTA CHAIN | ||||||
![]() | TRANSFERASE / SERINE/THREONINE-PROTEIN KINASE / SERINE-THREONINE KINASE / CELLULAR DIFFERENTIATION / VASCULAR SMOOTH MUSCLE / KINASE / ATP-BINDING / PHOSPHOPROTEIN / CALMODULIN-BINDING / NUCLEOTIDE-BINDING | ||||||
Function / homology | ![]() 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 | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Roos, A.K. / Rellos, P. / Salah, E. / Pike, A.C.W. / Fedorov, O. / Pilka, E.S. / von Delft, F. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. ...Roos, A.K. / Rellos, P. / Salah, E. / Pike, A.C.W. / Fedorov, O. / Pilka, E.S. / von Delft, F. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Bountra, C. / Knapp, S. | ||||||
![]() | ![]() Title: Structure of the Camkiidelta/Calmodulin Complex Reveals the Molecular Mechanism of Camkii Kinase Activation. Authors: Rellos, P. / Pike, A.C.W. / Niesen, F.H. / Salah, E. / Lee, W.H. / von Delft, F. / Knapp, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 134.3 KB | Display | ![]() |
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PDB format | ![]() | 103.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 24.9 KB | Display | |
Data in CIF | ![]() | 33.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2ux0C ![]() 2v7oSC ![]() 2vz6C ![]() 2w2cC ![]() 2welC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 1 / Auth seq-ID: -1 - 309 / Label seq-ID: 1 - 301
NCS oper: (Code: given Matrix: (-0.501, -0.82, 0.275), Vector: |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 34253.457 Da / Num. of mol.: 2 / Fragment: KINASE DOMAIN, RESIDUES 11-309 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q13557, Ca2+/calmodulin-dependent protein kinase |
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-Non-polymers , 5 types, 105 molecules ![](data/chem/img/PO4.gif)
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![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/EPE.gif)
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#2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-CL / | #4: Chemical | ChemComp-EPE / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 57 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: 1.6 M NAKPO4 HEPES PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 22, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98248 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→45 Å / Num. obs: 39106 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Biso Wilson estimate: 58.2 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2V7O Resolution: 2.3→43.03 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.935 / SU B: 15.783 / SU ML: 0.193 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.262 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.32 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→43.03 Å
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Refine LS restraints |
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