+Open data
-Basic information
Entry | Database: PDB / ID: 7pu9 | |||||||||
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Title | Crystal structure of CaM in complex with CDZ (form 2) | |||||||||
Components | Calmodulin-1 | |||||||||
Keywords | METAL BINDING PROTEIN / Calmodulin / CDZ | |||||||||
Function / homology | Function and homology information CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation ...CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / 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) / negative regulation of calcium ion export across plasma membrane / organelle localization by membrane tethering / Activation of RAC1 downstream of NMDARs / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / CLEC7A (Dectin-1) induces NFAT activation / autophagosome membrane docking / positive regulation of ryanodine-sensitive calcium-release channel activity / Negative regulation of NMDA receptor-mediated neuronal transmission / regulation of cell communication by electrical coupling involved in cardiac conduction / Unblocking of NMDA receptors, glutamate binding and activation / negative regulation of peptidyl-threonine phosphorylation / Synthesis of IP3 and IP4 in the cytosol / Phase 0 - rapid depolarisation / protein phosphatase activator activity / RHO GTPases activate PAKs / positive regulation of cyclic-nucleotide phosphodiesterase activity / positive regulation of phosphoprotein phosphatase activity / Long-term potentiation / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / catalytic complex / DARPP-32 events / detection of calcium ion / negative regulation of ryanodine-sensitive calcium-release channel activity / Smooth Muscle Contraction / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction / calcium channel inhibitor activity / cellular response to interferon-beta / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Protein methylation / voltage-gated potassium channel complex / Activation of AMPK downstream of NMDARs / eNOS activation / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / regulation of calcium-mediated signaling / positive regulation of protein dephosphorylation / titin binding / regulation of ryanodine-sensitive calcium-release channel activity / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Ion homeostasis / positive regulation of protein autophosphorylation / sperm midpiece / calcium channel complex / substantia nigra development / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / protein serine/threonine kinase activator activity / sarcomere / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / VEGFR2 mediated vascular permeability / positive regulation of peptidyl-threonine phosphorylation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / VEGFR2 mediated cell proliferation / regulation of cytokinesis / Translocation of SLC2A4 (GLUT4) to the plasma membrane / spindle microtubule / RAF activation / positive regulation of receptor signaling pathway via JAK-STAT / positive regulation of protein serine/threonine kinase activity / Transcriptional activation of mitochondrial biogenesis / Stimuli-sensing channels / spindle pole / cellular response to type II interferon / response to calcium ion / RAS processing / calcium-dependent protein binding / Inactivation, recovery and regulation of the phototransduction cascade / 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 / G2/M transition of mitotic cell cycle / Signaling by BRAF and RAF1 fusions / Platelet degranulation / myelin sheath / Ca2+ pathway / RAF/MAP kinase cascade / vesicle / transmembrane transporter binding / Extra-nuclear estrogen signaling / G protein-coupled receptor signaling pathway Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.279 Å | |||||||||
Authors | Mechaly, A.E. / Leger, C. / Haouz, A. / Chenal, A. | |||||||||
Funding support | France, 2items
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Citation | Journal: Bmc Biol. / Year: 2022 Title: Dynamics and structural changes of calmodulin upon interaction with the antagonist calmidazolium. Authors: Leger, C. / Pitard, I. / Sadi, M. / Carvalho, N. / Brier, S. / Mechaly, A. / Raoux-Barbot, D. / Davi, M. / Hoos, S. / Weber, P. / Vachette, P. / Durand, D. / Haouz, A. / Guijarro, J.I. / Ladant, D. / Chenal, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7pu9.cif.gz | 76.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pu9.ent.gz | 57.1 KB | Display | PDB format |
PDBx/mmJSON format | 7pu9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pu/7pu9 ftp://data.pdbj.org/pub/pdb/validation_reports/pu/7pu9 | HTTPS FTP |
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-Related structure data
Related structure data | 7pszC 1ctrS C: citing same article (ref.) S: Starting model for refinement |
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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: 16721.350 Da / Num. of mol.: 1 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: Chemical | #3: Chemical | ChemComp-CA / #4: 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 Matthews: 2.25 Å3/Da / Density % sol: 45.38 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion / Details: 0.2 M CaCl2, 0.1 M Tris pH 8.5 and 25 %w/v PEG 4K |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.8266 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 7, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8266 Å / Relative weight: 1 |
Reflection | Resolution: 2.279→56.153 Å / Num. obs: 8009 / % possible obs: 100 % / Redundancy: 34.8 % / CC1/2: 1 / Rmerge(I) obs: 0.156 / Rpim(I) all: 0.027 / Rrim(I) all: 0.159 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 2.279→2.318 Å / Rmerge(I) obs: 2.112 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 395 / CC1/2: 0.882 / Rpim(I) all: 0.334 / Rrim(I) all: 2.139 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1CTR Resolution: 2.279→56.15 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.914 / SU R Cruickshank DPI: 0.344 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.429 / SU Rfree Blow DPI: 0.254 / SU Rfree Cruickshank DPI: 0.238
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Displacement parameters | Biso mean: 60.49 Å2
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Refine analyze | Luzzati coordinate error obs: 0.39 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.279→56.15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.28→2.32 Å
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Refinement TLS params. | Origin x: -9.827 Å / Origin y: 16.9688 Å / Origin z: 12.4669 Å
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Refinement TLS group | Selection details: { A|* } |