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Yorodumi- PDB-4byf: Crystal structure of human Myosin 1c in complex with calmodulin i... -
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-Basic information
Entry | Database: PDB / ID: 4byf | ||||||
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Title | Crystal structure of human Myosin 1c in complex with calmodulin in the pre-power stroke state | ||||||
Components |
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Keywords | HYDROLASE / MYO1C / GLUT4 EXOCYTOSIS / ATPASE / MOTOR PROTEIN | ||||||
Function / homology | Function and homology information stereocilium membrane / small GTPase binding => GO:0031267 / positive regulation of cellular response to insulin stimulus / microfilament motor activity => GO:0000146 / unconventional myosin complex / : / positive regulation of vascular endothelial growth factor signaling pathway / positive regulation of cell migration by vascular endothelial growth factor signaling pathway / : / establishment of protein localization to mitochondrial membrane ...stereocilium membrane / small GTPase binding => GO:0031267 / positive regulation of cellular response to insulin stimulus / microfilament motor activity => GO:0000146 / unconventional myosin complex / : / positive regulation of vascular endothelial growth factor signaling pathway / positive regulation of cell migration by vascular endothelial growth factor signaling pathway / : / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / vesicle transport along actin filament / protein targeting to membrane / regulation of bicellular tight junction assembly / 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 / regulation of synaptic vesicle endocytosis / Loss of phosphorylation of MECP2 at T308 / microfilament motor activity / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / negative regulation of high voltage-gated calcium channel activity / regulation of synaptic vesicle exocytosis / 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 / response to corticosterone / positive regulation of actin filament polymerization / Fc-gamma receptor signaling pathway involved in phagocytosis / positive regulation of ryanodine-sensitive calcium-release channel activity / Negative regulation of NMDA receptor-mediated neuronal transmission / nitric-oxide synthase binding / 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 / filamentous actin / protein phosphatase activator activity / RHO GTPases activate PAKs / microvillus / positive regulation of cyclic-nucleotide phosphodiesterase activity / brush border / positive regulation of phosphoprotein phosphatase activity / Long-term potentiation / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / adenylate cyclase binding / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / positive regulation of protein targeting to membrane / catalytic complex / DARPP-32 events / detection of calcium ion / protein targeting / mRNA transport / Smooth Muscle Contraction / negative regulation of ryanodine-sensitive calcium-release channel activity / lateral plasma membrane / RHO GTPases activate IQGAPs / cellular response to interferon-beta / regulation of cardiac muscle contraction / calcium channel inhibitor activity / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / positive regulation of DNA binding / Protein methylation / enzyme regulator activity / voltage-gated potassium channel complex / phosphatidylinositol 3-kinase binding / phagocytic vesicle / Activation of AMPK downstream of NMDARs / eNOS activation / nuclear pore / 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 / transcription initiation-coupled chromatin remodeling / sperm midpiece / response to amphetamine / calcium channel complex / activation of adenylate cyclase activity / substantia nigra development / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 Å | ||||||
Authors | Munnich, S. / Taft, M.H. / Pathan-Chhatbar, S. / Manstein, D.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2014 Title: Crystal Structure of Human Myosin 1C-the Motor in Glut4 Exocytosis: Implications for Ca(2+) Regulation and 14-3-3 Binding. Authors: Munnich, S. / Taft, M.H. / Manstein, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4byf.cif.gz | 704.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4byf.ent.gz | 583.9 KB | Display | PDB format |
PDBx/mmJSON format | 4byf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/by/4byf ftp://data.pdbj.org/pub/pdb/validation_reports/by/4byf | HTTPS FTP |
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-Related structure data
Related structure data | 1lkxS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 83939.688 Da / Num. of mol.: 2 / Fragment: MOTOR DOMAIN, RESIDUES 36-760 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFASTBAC DUAL / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: O00159, EC: 3.6.4.1 #2: Protein | Mass: 16852.545 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFASTBAC DUAL / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P62158, UniProt: P0DP23*PLUS #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 51.2 % / Description: NONE |
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Crystal grow | Details: 18% PEG3350, 0.2 M SODIUM MALONATE PH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0645 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 11, 2013 |
Radiation | Monochromator: SILICON (1 1 1) CHANNEL-CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0645 Å / Relative weight: 1 |
Reflection | Resolution: 2.74→47.94 Å / Num. obs: 51985 / % possible obs: 94 % / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Biso Wilson estimate: 62.9 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 2.74→2.84 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 2.15 / % possible all: 89 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1LKX Resolution: 2.74→47.94 Å / σ(F): 2 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 2 Å / VDW probe radii: 2 Å | ||||||||||||||||||
Displacement parameters | Biso mean: 58.8 Å2 | ||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.74→47.94 Å
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Refine LS restraints |
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