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Yorodumi- PDB-6bd1: Complex of 14-3-3 theta with an IRSp53 peptide phosphorylated at S366 -
+Open data
-Basic information
Entry | Database: PDB / ID: 6bd1 | ||||||
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Title | Complex of 14-3-3 theta with an IRSp53 peptide phosphorylated at S366 | ||||||
Components |
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Keywords | SIGNALING PROTEIN / phosphate binding protein / protein complex / cytoskeleton regulation / cell motility | ||||||
Function / homology | Function and homology information RHO GTPases activate PKNs / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Regulation of localization of FOXO transcription factors / Activation of BAD and translocation to mitochondria / neuron projection branch point / dendritic spine cytoplasm / negative regulation of monoatomic ion transmembrane transport / plasma membrane organization / TP53 Regulates Metabolic Genes / actin crosslink formation ...RHO GTPases activate PKNs / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Regulation of localization of FOXO transcription factors / Activation of BAD and translocation to mitochondria / neuron projection branch point / dendritic spine cytoplasm / negative regulation of monoatomic ion transmembrane transport / plasma membrane organization / TP53 Regulates Metabolic Genes / actin crosslink formation / positive regulation of dendritic spine morphogenesis / cellular response to L-glutamate / protein localization to synapse / cadherin binding involved in cell-cell adhesion / regulation of modification of postsynaptic actin cytoskeleton / cytoskeletal anchor activity / presynaptic cytosol / neuron projection terminus / proline-rich region binding / postsynaptic cytosol / small GTPase-mediated signal transduction / positive regulation of actin filament polymerization / dendrite development / postsynaptic density, intracellular component / actin filament bundle assembly / positive regulation of excitatory postsynaptic potential / CDC42 GTPase cycle / excitatory synapse / Regulation of localization of FOXO transcription factors / protein targeting / Activation of BAD and translocation to mitochondria / RHO GTPases Activate WASPs and WAVEs / RAC3 GTPase cycle / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / cellular response to epidermal growth factor stimulus / ruffle / RAC1 GTPase cycle / substantia nigra development / axonogenesis / 14-3-3 protein binding / dendritic shaft / secretory granule / filopodium / synaptic membrane / PDZ domain binding / Translocation of SLC2A4 (GLUT4) to the plasma membrane / transcription coregulator binding / regulation of actin cytoskeleton organization / TP53 Regulates Metabolic Genes / FCGR3A-mediated phagocytosis / adherens junction / regulation of synaptic plasticity / Schaffer collateral - CA1 synapse / protein localization / Regulation of actin dynamics for phagocytic cup formation / VEGFA-VEGFR2 Pathway / insulin receptor signaling pathway / lamellipodium / regulation of cell shape / scaffold protein binding / microtubule / transmembrane transporter binding / protein domain specific binding / focal adhesion / negative regulation of DNA-templated transcription / neuronal cell body / synapse / glutamatergic synapse / signal transduction / protein-containing complex / extracellular exosome / nucleoplasm / membrane / identical protein binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å | ||||||
Authors | Kast, D.J. / Dominguez, R. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2019 Title: Mechanism of IRSp53 inhibition by 14-3-3. Authors: Kast, D.J. / Dominguez, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6bd1.cif.gz | 375.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bd1.ent.gz | 310 KB | Display | PDB format |
PDBx/mmJSON format | 6bd1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bd/6bd1 ftp://data.pdbj.org/pub/pdb/validation_reports/bd/6bd1 | HTTPS FTP |
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-Related structure data
Related structure data | 6bcrC 6bcyC 6bd2C 6bqtC 2br9S 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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2 |
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Unit cell |
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-Components
-Protein / Protein/peptide , 2 types, 8 molecules ABEFCDGH
#1: Protein | Mass: 27795.234 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pTYB11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q3SZI4, UniProt: P27348*PLUS #2: Protein/peptide | Mass: 1529.652 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9UQB8*PLUS |
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-Non-polymers , 4 types, 416 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-PEG / #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: 2.53 Å3/Da / Density % sol: 51.47 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.125 M CaCl2, 12% Peg 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SEALED TUBE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å |
Detector | Type: APEX II CCD / Detector: CCD / Date: Feb 17, 2012 / Details: Quazar MX optics |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→29.421 Å / Num. obs: 45896 / % possible obs: 95.6 % / Redundancy: 5.5 % / Biso Wilson estimate: 23.21 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.058 / Net I/σ(I): 20 |
Reflection shell | Resolution: 2.35→2.43 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.205 / Mean I/σ(I) obs: 4.9 / Num. unique obs: 4330 / CC1/2: 0.889 / % possible all: 90.4 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2BR9 Resolution: 2.35→29.421 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 27.07
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 136.36 Å2 / Biso mean: 34.944 Å2 / Biso min: 10.57 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.35→29.421 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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