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Yorodumi- PDB-4hkc: 14-3-3-zeta in complex with S1011 phosphorylated integrin alpha-4... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hkc | ||||||
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Title | 14-3-3-zeta in complex with S1011 phosphorylated integrin alpha-4 peptide | ||||||
Components |
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Keywords | SIGNALING PROTEIN/PEPTIDE / 14-3-3 / all-helical protein / regulatory / alpha-4 integrin tail / phosphorylation / SIGNAL TRANSDUCTION / SIGNALING PROTEIN-PEPTIDE complex | ||||||
Function / homology | Function and homology information clathrin-dependent extracellular exosome endocytosis / immune response in gut-associated lymphoid tissue / cell-matrix adhesion involved in ameboidal cell migration / integrin alpha4-beta7 complex / negative regulation of protein homodimerization activity / cell-cell adhesion in response to extracellular stimulus / diapedesis / cell-cell adhesion mediated by integrin / integrin alpha4-beta1 complex / Golgi reassembly ...clathrin-dependent extracellular exosome endocytosis / immune response in gut-associated lymphoid tissue / cell-matrix adhesion involved in ameboidal cell migration / integrin alpha4-beta7 complex / negative regulation of protein homodimerization activity / cell-cell adhesion in response to extracellular stimulus / diapedesis / cell-cell adhesion mediated by integrin / integrin alpha4-beta1 complex / Golgi reassembly / positive regulation of leukocyte tethering or rolling / axonogenesis involved in innervation / regulation of synapse maturation / NOTCH4 Activation and Transmission of Signal to the Nucleus / protein antigen binding / establishment of Golgi localization / leukocyte tethering or rolling / RUNX3 Regulates Immune Response and Cell Migration / Rap1 signalling / positive regulation of endothelial cell apoptotic process / heterotypic cell-cell adhesion / negative regulation of protein localization to nucleus / integrin complex / positive regulation of vascular endothelial cell proliferation / cell adhesion mediated by integrin / neuron projection extension / KSRP (KHSRP) binds and destabilizes mRNA / leukocyte cell-cell adhesion / negative regulation of vasoconstriction / GP1b-IX-V activation signalling / receptor clustering / endodermal cell differentiation / cellular response to cytokine stimulus / fibronectin binding / Regulation of localization of FOXO transcription factors / Interleukin-3, Interleukin-5 and GM-CSF signaling / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / positive regulation of T cell migration / cellular response to glucose starvation / Integrin cell surface interactions / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / coreceptor activity / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / negative regulation of TORC1 signaling / cell adhesion molecule binding / cell-matrix adhesion / negative regulation of innate immune response / substrate adhesion-dependent cell spreading / protein sequestering activity / regulation of ERK1 and ERK2 cascade / B cell differentiation / integrin-mediated signaling pathway / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Deactivation of the beta-catenin transactivating complex / Cell surface interactions at the vascular wall / TP53 Regulates Metabolic Genes / Negative regulation of NOTCH4 signaling / cell-cell adhesion / cellular response to amyloid-beta / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / melanosome / integrin binding / growth cone / blood microparticle / DNA-binding transcription factor binding / vesicle / Potential therapeutics for SARS / transmembrane transporter binding / cadherin binding / external side of plasma membrane / protein phosphorylation / focal adhesion / neuronal cell body / glutamatergic synapse / ubiquitin protein ligase binding / negative regulation of apoptotic process / protein kinase binding / negative regulation of transcription by RNA polymerase II / cell surface / signal transduction / extracellular space / RNA binding / extracellular exosome / nucleoplasm / membrane / identical protein binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Bonet, R. / Campbell, I.D. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2013 Title: Characterization of 14-3-3-zeta Interactions with integrin tails Authors: Bonet, R. / Vakonakis, I. / Campbell, I.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hkc.cif.gz | 111.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hkc.ent.gz | 85.5 KB | Display | PDB format |
PDBx/mmJSON format | 4hkc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hk/4hkc ftp://data.pdbj.org/pub/pdb/validation_reports/hk/4hkc | HTTPS FTP |
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-Related structure data
Related structure data | 2o02S S: Starting model for refinement |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28188.545 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: N-terminal His-tag followed by a 3C protease cleavage site Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAZ / Plasmid: pET16-b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P63104 |
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#2: Protein/peptide | Mass: 3797.991 Da / Num. of mol.: 1 / Fragment: UNP residues 1003-1032 / Source method: obtained synthetically Details: Chemically synthesized peptide corresponding to alpha-4 integrin tail Source: (synth.) Homo sapiens (human) / References: UniProt: P13612 |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.6 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M Na HEPES (pH 7.5), 25% PEG 2000 MME, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9163 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 28, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9163 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→44.5 Å / Num. all: 18798 / Num. obs: 18798 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Biso Wilson estimate: 49.47 Å2 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.394 / Mean I/σ(I) obs: 3.2 / Num. unique all: 2725 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2O02 Resolution: 2.2→34.8 Å / Cor.coef. Fo:Fc: 0.9507 / Cor.coef. Fo:Fc free: 0.9375 / SU R Cruickshank DPI: 0.192 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 60.17 Å2
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Refine analyze | Luzzati coordinate error obs: 0.357 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→34.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.33 Å / Total num. of bins used: 9
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Refinement TLS params. | Method: refined / Origin x: 22.1337 Å / Origin y: 7.89 Å / Origin z: 17.4031 Å
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Refinement TLS group | Selection details: { A|2 - A|230 } |