+Open data
-Basic information
Entry | Database: PDB / ID: 3o78 | ||||||
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Title | The structure of Ca2+ Sensor (Case-12) | ||||||
Components | Myosin light chain kinase, smooth muscle,Green fluorescent protein,Green fluorescent protein,Calmodulin-1 | ||||||
Keywords | FLUORESCENT PROTEIN / circular permutated green fluorescent protein / genetically encoded / GFP Calmodulin M13-peptide / Calcium sensor / M13-peptide / GYG naturally modified tripeptide acts as chromophore | ||||||
Function / homology | Function and homology information tonic smooth muscle contraction / myosin-light-chain kinase / myosin light chain kinase activity / muscle structure development / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Reduction of cytosolic Ca++ levels / Calmodulin induced events / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde ...tonic smooth muscle contraction / myosin-light-chain kinase / myosin light chain kinase activity / muscle structure development / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Reduction of cytosolic Ca++ levels / Calmodulin induced events / 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 / organelle localization by membrane tethering / negative regulation of high voltage-gated calcium channel activity / CaMK IV-mediated phosphorylation of CREB / autophagosome membrane docking / mitochondrion-endoplasmic reticulum membrane tethering / Glycogen breakdown (glycogenolysis) / positive regulation of cyclic-nucleotide phosphodiesterase activity / negative regulation of calcium ion export across plasma membrane / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / regulation of cardiac muscle cell action potential / positive regulation of ryanodine-sensitive calcium-release channel activity / regulation of cell communication by electrical coupling involved in cardiac conduction / Synthesis of IP3 and IP4 in the cytosol / negative regulation of peptidyl-threonine phosphorylation / Negative regulation of NMDA receptor-mediated neuronal transmission / Phase 0 - rapid depolarisation / Unblocking of NMDA receptors, glutamate binding and activation / negative regulation of ryanodine-sensitive calcium-release channel activity / adenylate cyclase activator activity / protein phosphatase activator activity / RHO GTPases activate PAKs / Ion transport by P-type ATPases / cleavage furrow / : / Uptake and function of anthrax toxins / Long-term potentiation / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / catalytic complex / DARPP-32 events / regulation of cardiac muscle contraction / detection of calcium ion / Smooth Muscle Contraction / regulation of ryanodine-sensitive calcium-release channel activity / cellular response to interferon-beta / RHO GTPases activate IQGAPs / calcium channel inhibitor activity / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / eNOS activation / Protein methylation / voltage-gated potassium channel complex / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Activation of AMPK downstream of NMDARs / stress fiber / Ion homeostasis / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / : / titin binding / positive regulation of protein autophosphorylation / regulation of calcium-mediated signaling / sperm midpiece / calcium channel complex / substantia nigra development / Ras activation upon Ca2+ influx through NMDA receptor / sarcomere / regulation of heart rate / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / protein serine/threonine kinase activator activity / bioluminescence / VEGFR2 mediated vascular permeability / regulation of cytokinesis / VEGFR2 mediated cell proliferation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / positive regulation of peptidyl-threonine phosphorylation / generation of precursor metabolites and energy / spindle microtubule / Translocation of SLC2A4 (GLUT4) to the plasma membrane / positive regulation of receptor signaling pathway via JAK-STAT / RAF activation / Transcriptional activation of mitochondrial biogenesis / positive regulation of protein serine/threonine kinase activity / Stimuli-sensing channels / cellular response to type II interferon / spindle pole / response to calcium ion / RAS processing / 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 / calcium-dependent protein binding / G2/M transition of mitotic cell cycle / Signaling by BRAF and RAF1 fusions / Inactivation, recovery and regulation of the phototransduction cascade Similarity search - Function | ||||||
Biological species | Gallus gallus (chicken) Aequorea victoria (jellyfish) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Leder, L. / Stark, W. / Freuler, F. / Marsh, M. / Meyerhofer, M. / Stettler, T. / Mayr, L.M. / Britanova, O.V. / Strukova, L.A. / Chudakov, D.M. | ||||||
Citation | Journal: Sensors (Basel) / Year: 2010 Title: The structure of Ca2+ sensor Case16 reveals the mechanism of reaction to low Ca2+ concentrations Authors: Leder, L. / Stark, W. / Freuler, F. / Marsh, M. / Meyerhofer, M. / Stettler, T. / Mayr, L.M. / Britanova, O.V. / Strukova, L.A. / Chudakov, D.M. / Souslova, E.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3o78.cif.gz | 173.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3o78.ent.gz | 136 KB | Display | PDB format |
PDBx/mmJSON format | 3o78.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3o78_validation.pdf.gz | 459 KB | Display | wwPDB validaton report |
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Full document | 3o78_full_validation.pdf.gz | 495.8 KB | Display | |
Data in XML | 3o78_validation.xml.gz | 35.2 KB | Display | |
Data in CIF | 3o78_validation.cif.gz | 47.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o7/3o78 ftp://data.pdbj.org/pub/pdb/validation_reports/o7/3o78 | HTTPS FTP |
-Related structure data
Related structure data | 3o77SC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Refine code: 1
NCS ensembles :
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-Components
#1: Protein | Mass: 46491.883 Da / Num. of mol.: 2 / Mutation: POINT MUTATIONS Source method: isolated from a genetically manipulated source Details: Chimera protein of peptide of M13 (residues 1730-1749, UNP P11799), C-terminal domain of Green fluorescent protein (residues 147-238, UNP P42212), linker, N-terminal of Green fluorescent ...Details: Chimera protein of peptide of M13 (residues 1730-1749, UNP P11799), C-terminal domain of Green fluorescent protein (residues 147-238, UNP P42212), linker, N-terminal of Green fluorescent protein (residues 2-146, UNP P42212) and residues 3-149 of Calmodulin (UNP P0DP23) Source: (gene. exp.) Gallus gallus (chicken), (gene. exp.) Aequorea victoria (jellyfish), (gene. exp.) Homo sapiens (human) Gene: Mylk, GFP, CALM1, CALM, CAM, CAM1 / Plasmid: pET41 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Tuner References: UniProt: P11799, UniProt: P42212, UniProt: P0DP23, myosin-light-chain kinase #2: Chemical | ChemComp-CA / #3: Water | ChemComp-HOH / | Sequence details | UNP RESIDUE 65 SER AND 72 SER OF GREEN FLUORESCENT PROTEIN IN DATABASE UNP P42212 (GFP_AEQVI) ...UNP RESIDUE 65 SER AND 72 SER OF GREEN FLUORESCEN | |
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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: 2.08 Å3/Da / Density % sol: 40.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: Reservoir: 100mM Tris HCL (pH 5.5), 100mM (NH4)2SO4, 21% PEG 3350; Protein stock: 7.6 mg/ml Protein, 50mM Tris HCl (pH 7.4), 150mM NaCl; Seed stock solution: 20mM CaCl2, 20% PEG 3350, VAPOR ...Details: Reservoir: 100mM Tris HCL (pH 5.5), 100mM (NH4)2SO4, 21% PEG 3350; Protein stock: 7.6 mg/ml Protein, 50mM Tris HCl (pH 7.4), 150mM NaCl; Seed stock solution: 20mM CaCl2, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54179 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 20, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→100 Å / Num. obs: 23464 / % possible obs: 99.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 41.9 Å2 / Rsym value: 0.101 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.6→2.71 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.517 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3O77 Resolution: 2.6→50.83 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.84 / SU B: 24.1 / SU ML: 0.376 / Cross valid method: THROUGHOUT / ESU R Free: 0.45 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.432 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→50.83 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION / Type: tight positional / Weight position: 0.05
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LS refinement shell | Resolution: 2.6→2.667 Å / Total num. of bins used: 20
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