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- PDB-7zrp: 2.65 Angstrom crystal structure of Ca/CaM:CaMKIIdelta peptide complex -
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Open data
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Basic information
Entry | Database: PDB / ID: 7zrp | |||||||||
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Title | 2.65 Angstrom crystal structure of Ca/CaM:CaMKIIdelta peptide complex | |||||||||
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![]() | METAL BINDING PROTEIN / calcium-binding protein / calmodulin / CaM / CaMKII / kinase | |||||||||
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 / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / relaxation of cardiac muscle / Calmodulin induced events / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / Reduction of cytosolic Ca++ levels / calcium/calmodulin-dependent protein kinase activity / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Activation of Ca-permeable Kainate Receptor / 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) / regulation of heart contraction / positive regulation of cyclic-nucleotide phosphodiesterase activity / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / CLEC7A (Dectin-1) induces NFAT activation / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / Activation of RAC1 downstream of NMDARs / positive regulation of ryanodine-sensitive calcium-release channel activity / 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 / negative regulation of peptidyl-threonine phosphorylation / Synthesis of IP3 and IP4 in the cytosol / Unblocking of NMDA receptors, glutamate binding and activation / Phase 0 - rapid depolarisation / protein phosphatase activator activity / regulation of heart rate by cardiac conduction / RHO GTPases activate PAKs / positive regulation of phosphoprotein phosphatase activity / Ion transport by P-type ATPases / Long-term potentiation / Uptake and function of anthrax toxins / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / HSF1-dependent transactivation / catalytic complex / DARPP-32 events / detection of calcium ion / regulation of cardiac muscle contraction / negative regulation of ryanodine-sensitive calcium-release channel activity / Smooth Muscle Contraction / calcium channel inhibitor activity / RHO GTPases activate IQGAPs / cellular response to interferon-beta / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Protein methylation / eNOS activation / Activation of AMPK downstream of NMDARs / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / positive regulation of protein dephosphorylation / Ion homeostasis / regulation of calcium-mediated signaling / regulation of ryanodine-sensitive calcium-release channel activity / titin binding / positive regulation of protein autophosphorylation / voltage-gated potassium channel complex / sperm midpiece / sarcoplasmic reticulum membrane / calcium channel complex / cellular response to calcium ion / substantia nigra development / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / sarcomere / protein serine/threonine kinase activator activity / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / VEGFR2 mediated vascular permeability / regulation of cytokinesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / positive regulation of peptidyl-threonine phosphorylation / VEGFR2 mediated cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / regulation of cell growth Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Helassa, N. / Antonyuk, S. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Calmodulin variant E140G associated with long QT syndrome impairs CaMKII delta autophosphorylation and L-type calcium channel inactivation. Authors: Prakash, O. / Gupta, N. / Milburn, A. / McCormick, L. / Deugi, V. / Fisch, P. / Wyles, J. / Thomas, N.L. / Antonyuk, S. / Dart, C. / Helassa, N. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 145.6 KB | Display | ![]() |
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PDB format | ![]() | 112 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 663.5 KB | Display | ![]() |
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Full document | ![]() | 669.2 KB | Display | |
Data in XML | ![]() | 15 KB | Display | |
Data in CIF | ![]() | 19.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7zrqC ![]() 2welS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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Components
-Protein / Protein/peptide , 2 types, 4 molecules ACBD
#1: Protein | Mass: 16721.350 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 2515.011 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() References: UniProt: Q13557, Ca2+/calmodulin-dependent protein kinase |
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-Non-polymers , 5 types, 57 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
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#3: Chemical | ChemComp-CA / #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-ZN / #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.47 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop Details: 200 mM Zinc acetate, 100 mM Imidazole pH8.0, 18% PEG3000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 11, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→53.25 Å / Num. obs: 11133 / % possible obs: 100 % / Redundancy: 5.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.102 / Rrim(I) all: 0.185 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 2.65→2.78 Å / Redundancy: 6.1 % / Rmerge(I) obs: 1.921 / Num. unique obs: 1442 / CC1/2: 0.576 / Rpim(I) all: 1.249 / Rrim(I) all: 2.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2WEL Resolution: 2.65→53.244 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.905 / WRfactor Rfree: 0.272 / WRfactor Rwork: 0.205 / SU B: 18.34 / SU ML: 0.356 / Average fsc free: 0.9334 / Average fsc work: 0.9573 / Cross valid method: THROUGHOUT / ESU R Free: 0.373 Details: Hydrogens have been added in their 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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 66.088 Å2
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Refinement step | Cycle: LAST / Resolution: 2.65→53.244 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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