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Yorodumi- PDB-7zrq: 1.68 Angstrom crystal structure of Ca/CaM-E140G:CaMKIIdelta pepti... -
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-Basic information
Entry | Database: PDB / ID: 7zrq | |||||||||
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Title | 1.68 Angstrom crystal structure of Ca/CaM-E140G:CaMKIIdelta peptide complex | |||||||||
Components |
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Keywords | METAL BINDING PROTEIN / calcium-binding protein / calmodulin / CaM / CaMKII / kinase | |||||||||
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 / endoplasmic reticulum calcium ion homeostasis / cardiac muscle cell contraction / 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) / positive regulation of cyclic-nucleotide phosphodiesterase activity / regulation of heart contraction / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / CLEC7A (Dectin-1) induces NFAT activation / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / regulation of cardiac muscle cell action potential / 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 / negative regulation of ryanodine-sensitive calcium-release channel activity / protein phosphatase activator activity / regulation of heart rate by cardiac conduction / RHO GTPases activate PAKs / : / Ion transport by P-type ATPases / Long-term potentiation / Uptake and function of anthrax toxins / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / catalytic complex / HSF1-dependent transactivation / DARPP-32 events / detection of calcium ion / regulation of cardiac muscle contraction / regulation of ryanodine-sensitive calcium-release channel activity / Smooth Muscle Contraction / cellular response to interferon-beta / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium channel inhibitor activity / Protein methylation / eNOS activation / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Activation of AMPK downstream of NMDARs / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / : / Ion homeostasis / titin binding / regulation of calcium-mediated signaling / positive regulation of protein autophosphorylation / voltage-gated potassium channel complex / sperm midpiece / sarcoplasmic reticulum membrane / calcium channel complex / substantia nigra development / cellular response to calcium ion / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / sarcomere / FCERI mediated Ca+2 mobilization / protein serine/threonine kinase activator activity / FCGR3A-mediated IL10 synthesis / VEGFR2 mediated vascular permeability / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / VEGFR2 mediated cell proliferation / regulation of cytokinesis / positive regulation of peptidyl-threonine phosphorylation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / spindle microtubule Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å | |||||||||
Authors | Helassa, N. / Antonyuk, S. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: J.Biol.Chem. / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zrq.cif.gz | 79.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zrq.ent.gz | 57.2 KB | Display | PDB format |
PDBx/mmJSON format | 7zrq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zr/7zrq ftp://data.pdbj.org/pub/pdb/validation_reports/zr/7zrq | HTTPS FTP |
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-Related structure data
Related structure data | 7zrpC 2welS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16649.287 Da / Num. of mol.: 1 / Mutation: E140G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CALM1, CALM, CAM, CAM1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DP23 | ||||||
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#2: Protein/peptide | Mass: 2515.011 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) References: UniProt: Q13557, Ca2+/calmodulin-dependent protein kinase | ||||||
#3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density % sol: 27.04 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop Details: 0.1 M Na+-HEPES, 0.1 M MOPS (acid), pH 7.5, 0.03 M magnesium chloride hexahydrate, 0.03 M calcium chloride dihydrate, 12.5% v/v MPD; 12.5% PEG 1000; 12.5% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
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: 1.68→39.59 Å / Num. obs: 15287 / % possible obs: 99.1 % / Redundancy: 6.3 % / CC1/2: 1 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.03 / Rrim(I) all: 0.057 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 1.68→1.71 Å / Redundancy: 4.6 % / Rmerge(I) obs: 2.042 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 684 / CC1/2: 0.311 / Rpim(I) all: 1.452 / Rrim(I) all: 2.522 / % possible all: 87.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2WEL Resolution: 1.68→39.59 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.962 / SU B: 9.797 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.128 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: 29.842 Å2
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Refinement step | Cycle: LAST / Resolution: 1.68→39.59 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Selection: ALL |