+Open data
-Basic information
Entry | Database: PDB / ID: 5wsv | ||||||
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Title | Crystal structure of Myosin VIIa IQ5 in complex with Ca2+-CaM | ||||||
Components |
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Keywords | MOTOR PROTEIN/CALCIUM BINDING PROTEIN / Molecular motor / Calcium signaling / Protein complex / Calmodulin / MOTOR PROTEIN-CALCIUM BINDING PROTEIN complex | ||||||
Function / homology | Function and homology information pigment granule localization / upper tip-link density / pigment granule transport / The canonical retinoid cycle in rods (twilight vision) / myosin VII complex / stereocilium base / inner ear receptor cell differentiation / phagolysosome assembly / equilibrioception / sensory perception of light stimulus ...pigment granule localization / upper tip-link density / pigment granule transport / The canonical retinoid cycle in rods (twilight vision) / myosin VII complex / stereocilium base / inner ear receptor cell differentiation / phagolysosome assembly / equilibrioception / sensory perception of light stimulus / mechanoreceptor differentiation / photoreceptor connecting cilium / inner ear receptor cell stereocilium organization / sensory organ development / actin filament-based movement / inner ear auditory receptor cell differentiation / : / sensory perception / establishment of protein localization to mitochondrial membrane / stereocilium / cell projection organization / type 3 metabotropic glutamate receptor binding / myosin complex / auditory receptor cell stereocilium organization / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / regulation of synaptic vesicle endocytosis / Reduction of cytosolic Ca++ levels / 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) / inner ear morphogenesis / positive regulation of cyclic-nucleotide phosphodiesterase activity / regulation of synaptic vesicle exocytosis / 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 / microfilament motor activity / regulation of cardiac muscle cell action potential / Activation of RAC1 downstream of NMDARs / spectrin binding / response to corticosterone / positive regulation of DNA binding / cochlea development / lysosome organization / positive regulation of ryanodine-sensitive calcium-release channel activity / nitric-oxide synthase binding / 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 / RHO GTPases activate PAKs / cytoskeletal motor activity / : / Ion transport by P-type ATPases / microvillus / inner ear development / Long-term potentiation / Uptake and function of anthrax toxins / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / adenylate cyclase binding / catalytic complex / DARPP-32 events / detection of calcium ion / regulation of cardiac muscle contraction / photoreceptor outer segment / 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 / phosphatidylinositol 3-kinase binding / eNOS activation / phagocytosis / enzyme regulator activity / activation of adenylate cyclase activity / 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 Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å | ||||||
Authors | Li, J. / Chen, Y. / Deng, Y. / Lu, Q. / Zhang, M. | ||||||
Citation | Journal: Structure / Year: 2017 Title: Ca(2+)-Induced Rigidity Change of the Myosin VIIa IQ Motif-Single alpha Helix Lever Arm Extension Authors: Li, J. / Chen, Y. / Deng, Y. / Unarta, I.C. / Lu, Q. / Huang, X. / Zhang, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wsv.cif.gz | 142.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wsv.ent.gz | 109.8 KB | Display | PDB format |
PDBx/mmJSON format | 5wsv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ws/5wsv ftp://data.pdbj.org/pub/pdb/validation_reports/ws/5wsv | HTTPS FTP |
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-Related structure data
Related structure data | 5wstC 5wsuC 3g43S C: citing same article (ref.) 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: 16950.584 Da / Num. of mol.: 2 / Fragment: UNP residues 1-147 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Gene: CALM1, CALM, CAM, CAM1, CALM2, CAM2, CAMB, CALM3, CALML2, CAM3, CAMC, CAMIII Production host: Escherichia coli (E. coli) / References: UniProt: P62158, UniProt: P0DP23*PLUS #2: Protein/peptide | Mass: 5658.692 Da / Num. of mol.: 2 / Fragment: UNP residues 828-870 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Myo7a, Myo7 / Production host: Escherichia coli (E. coli) / References: UniProt: P97479 #3: Chemical | ChemComp-CA / #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: 1.69 Å3/Da / Density % sol: 27.1 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion / pH: 6.5 Details: 0.2M ammonium sulfate, 0.1M Bis-Tris (pH 6.5), 25%(w/v) PEG 3,500 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 12, 2014 |
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.33→50 Å / Num. obs: 12459 / % possible obs: 97.5 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 23 |
Reflection shell | Resolution: 2.35→2.39 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 4.1 / Rsym value: 0.36 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3G43 Resolution: 2.33→44.88 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.897 / SU B: 25.713 / SU ML: 0.282 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.643 / ESU R Free: 0.289 Details: U VALUES : WITH TLS ADDED 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 93.27 Å2 / Biso mean: 45.433 Å2 / Biso min: 23.49 Å2
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Refinement step | Cycle: final / Resolution: 2.33→44.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.329→2.389 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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