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Yorodumi- PDB-5myc: Crystal structure of human 14-3-3 sigma in complex with LRRK2 pep... -
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-Basic information
Entry | Database: PDB / ID: 5myc | |||||||||
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Title | Crystal structure of human 14-3-3 sigma in complex with LRRK2 peptide pS910 | |||||||||
Components |
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Keywords | TRANSFERASE / 14-3-3 LRRK2 phosphorylation PPI | |||||||||
Function / homology | Function and homology information peroxidase inhibitor activity / caveola neck / negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation / negative regulation of protein processing involved in protein targeting to mitochondrion / Wnt signalosome assembly / beta-catenin destruction complex binding / regulation of branching morphogenesis of a nerve / regulation of kidney size / regulation of neuron maturation / tangential migration from the subventricular zone to the olfactory bulb ...peroxidase inhibitor activity / caveola neck / negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation / negative regulation of protein processing involved in protein targeting to mitochondrion / Wnt signalosome assembly / beta-catenin destruction complex binding / regulation of branching morphogenesis of a nerve / regulation of kidney size / regulation of neuron maturation / tangential migration from the subventricular zone to the olfactory bulb / protein localization to endoplasmic reticulum exit site / GTP-dependent protein kinase activity / regulation of neuroblast proliferation / regulation of ER to Golgi vesicle-mediated transport / regulation of synaptic vesicle transport / negative regulation of late endosome to lysosome transport / regulation of mitochondrial depolarization / negative regulation of protein targeting to mitochondrion / positive regulation of dopamine receptor signaling pathway / regulation of lysosomal lumen pH / regulation of CAMKK-AMPK signaling cascade / amphisome / mitochondrion localization / cytoplasmic side of mitochondrial outer membrane / multivesicular body, internal vesicle / co-receptor binding / regulation of retrograde transport, endosome to Golgi / negative regulation of excitatory postsynaptic potential / negative regulation of autophagosome assembly / regulation of dopamine receptor signaling pathway / positive regulation of microglial cell activation / neuron projection arborization / positive regulation of synaptic vesicle endocytosis / JUN kinase kinase kinase activity / olfactory bulb development / regulation of dendritic spine morphogenesis / regulation of protein kinase A signaling / striatum development / protein localization to mitochondrion / cellular response to dopamine / presynaptic cytosol / positive regulation of protein autoubiquitination / endoplasmic reticulum organization / Wnt signalosome / GTP metabolic process / positive regulation of programmed cell death / regulation of canonical Wnt signaling pathway / negative regulation of protein processing / syntaxin-1 binding / regulation of reactive oxygen species metabolic process / exploration behavior / negative regulation of GTPase activity / protein kinase A binding / regulation of locomotion / autolysosome / regulation of synaptic vesicle exocytosis / Golgi-associated vesicle / PTK6 promotes HIF1A stabilization / clathrin binding / negative regulation of macroautophagy / lysosome organization / regulation of mitochondrial fission / neuromuscular junction development / locomotory exploration behavior / intracellular distribution of mitochondria / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / Golgi organization / positive regulation of nitric-oxide synthase biosynthetic process / microvillus / Rho protein signal transduction / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / cellular response to organic cyclic compound / MAP kinase kinase kinase activity / phosphoserine residue binding / canonical Wnt signaling pathway / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / positive regulation of protein kinase activity / establishment of skin barrier / cellular response to manganese ion / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / endoplasmic reticulum exit site / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / positive regulation of autophagy / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / protein kinase A signaling / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / JNK cascade / regulation of synaptic transmission, glutamatergic / excitatory postsynaptic potential / cellular response to starvation / dendrite cytoplasm / regulation of membrane potential Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.459 Å | |||||||||
Authors | Stevers, L.M. / de Vries, R.M.J.M. / Ottmann, C. | |||||||||
Citation | Journal: Biochem. J. / Year: 2017 Title: Structural interface between LRRK2 and 14-3-3 protein. Authors: Stevers, L.M. / de Vries, R.M. / Doveston, R.G. / Milroy, L.G. / Brunsveld, L. / Ottmann, C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5myc.cif.gz | 79.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5myc.ent.gz | 57.1 KB | Display | PDB format |
PDBx/mmJSON format | 5myc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/my/5myc ftp://data.pdbj.org/pub/pdb/validation_reports/my/5myc | HTTPS FTP |
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-Related structure data
Related structure data | 5my9C 5btvS 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein / Protein/peptide , 2 types, 2 molecules AP
#1: Protein | Mass: 26542.914 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SFN, HME1 / Production host: Escherichia coli (E. coli) / References: UniProt: P31947 |
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#2: Protein/peptide | Mass: 4458.819 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) References: UniProt: Q5S007, non-specific serine/threonine protein kinase |
-Non-polymers , 4 types, 417 molecules
#3: Chemical | #4: Chemical | ChemComp-CL / | #5: Chemical | ChemComp-NA / | #6: 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: 2.34 Å3/Da / Density % sol: 47.54 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.3 / Details: HEPES, NaCl2, PEG400, Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97862 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 26, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97862 Å / Relative weight: 1 |
Reflection | Resolution: 1.088→45.618 Å / Num. obs: 116840 / % possible obs: 99.7 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.035 / Rrim(I) all: 0.129 / Net I/σ(I): 14.99 |
Reflection shell | Resolution: 1.46→1.54 Å / Redundancy: 11.8 % / Rmerge(I) obs: 1.086 / Mean I/σ(I) obs: 2.2 / Num. measured obs: 85995 / CC1/2: 0.75 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5BTV Resolution: 1.459→41.848 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.55
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.459→41.848 Å
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Refine LS restraints |
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LS refinement shell |
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