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Yorodumi- PDB-2v7d: 14-3-3 protein zeta in complex with Thr758 phosphorylated integri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2v7d | ||||||
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Title | 14-3-3 protein zeta in complex with Thr758 phosphorylated integrin beta2 peptide | ||||||
Components |
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Keywords | SIGNALING PROTEIN / MEMBRANE / INTEGRIN / RECEPTOR / CYTOPLASM / ACETYLATION / TRANSMEMBRANE / BETA2 INTEGRIN / PHOSPHORYLATION / DISEASE MUTATION / PYRROLIDONE CARBOXYLIC ACID / 14-3-3 ZETA / GLYCOPROTEIN / CELL ADHESION | ||||||
Function / homology | Function and homology information KSRP (KHSRP) binds and destabilizes mRNA / RHO GTPases activate PKNs / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / NOTCH4 Activation and Transmission of Signal to the Nucleus / Regulation of localization of FOXO transcription factors / Activation of BAD and translocation to mitochondria / synaptic target recognition / integrin alphaX-beta2 complex / : / cellular extravasation ...KSRP (KHSRP) binds and destabilizes mRNA / RHO GTPases activate PKNs / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / NOTCH4 Activation and Transmission of Signal to the Nucleus / Regulation of localization of FOXO transcription factors / Activation of BAD and translocation to mitochondria / synaptic target recognition / integrin alphaX-beta2 complex / : / cellular extravasation / GP1b-IX-V activation signalling / integrin alphaM-beta2 complex / positive regulation of prostaglandin-E synthase activity / positive regulation of neutrophil degranulation / integrin alphaL-beta2 complex / ICAM-3 receptor activity / Deactivation of the beta-catenin transactivating complex / respiratory system process / neutrophil degranulation / : / Rap1 signalling / TP53 Regulates Metabolic Genes / complement component C3b binding / regulation of programmed cell death / neutrophil migration / Toll Like Receptor 4 (TLR4) Cascade / Interleukin-3, Interleukin-5 and GM-CSF signaling / leukocyte migration involved in inflammatory response / negative regulation of dopamine metabolic process / cell-cell adhesion via plasma-membrane adhesion molecules / tube formation / natural killer cell activation / heterotypic cell-cell adhesion / integrin complex / positive regulation of leukocyte adhesion to vascular endothelial cell / cell adhesion mediated by integrin / toll-like receptor 4 signaling pathway / phagocytosis, engulfment / leukocyte cell-cell adhesion / leukocyte migration / receptor clustering / amyloid-beta clearance / endodermal cell differentiation / plasma membrane raft / tertiary granule membrane / ficolin-1-rich granule membrane / cellular response to low-density lipoprotein particle stimulus / positive regulation of protein targeting to membrane / phosphoserine residue binding / protein targeting / endothelial cell migration / regulation of immune response / Integrin cell surface interactions / specific granule membrane / regulation of peptidyl-tyrosine phosphorylation / ERK1 and ERK2 cascade / heat shock protein binding / hippocampal mossy fiber to CA3 synapse / receptor-mediated endocytosis / cell adhesion molecule binding / extracellular matrix organization / cell-matrix adhesion / regulation of ERK1 and ERK2 cascade / neutrophil chemotaxis / protein sequestering activity / positive regulation of superoxide anion generation / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / microglial cell activation / lung development / receptor internalization / cell-cell adhesion / cytokine-mediated signaling pathway / positive regulation of angiogenesis / extracellular vesicle / positive regulation of nitric oxide biosynthetic process / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / melanosome / cell migration / integrin binding / cell-cell signaling / amyloid-beta binding / positive regulation of NF-kappaB transcription factor activity / regulation of cell shape / angiogenesis / Interleukin-4 and Interleukin-13 signaling / receptor complex / cell adhesion / inflammatory response / protein domain specific binding / external side of plasma membrane / protein phosphorylation / focal adhesion / apoptotic process / Neutrophil degranulation / protein kinase binding / negative regulation of transcription by RNA polymerase II / cell surface / signal transduction / extracellular exosome Similarity search - Function | ||||||
Biological species | BOS TAURUS (cattle) HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Takala, H. / Ylanne, J. | ||||||
Citation | Journal: Blood / Year: 2008 Title: Beta2 Integrin Phosphorylation on Thr758 Acts as a Molecular Switch to Regulate 14-3-3 and Filamin Binding. Authors: Takala, H. / Nurminen, E. / Nurmi, S.M. / Aatonen, M. / Strandin, T. / Takatalo, M. / Kiema, T. / Gahmberg, C.G. / Ylanne, J. / Fagerholm, S.C. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2v7d.cif.gz | 195.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v7d.ent.gz | 157.7 KB | Display | PDB format |
PDBx/mmJSON format | 2v7d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v7/2v7d ftp://data.pdbj.org/pub/pdb/validation_reports/v7/2v7d | HTTPS FTP |
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-Related structure data
Related structure data | 2jf1C 1a4oS 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 oper:
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-Components
#1: Protein | Mass: 27921.221 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BOS TAURUS (cattle) / Plasmid: PET-15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P63103 #2: Protein/peptide | Mass: 1130.186 Da / Num. of mol.: 4 / Fragment: INTEGRIN CYTOPLASMIC TAIL, RESIDUES 755-764 / Source method: obtained synthetically / Details: THR758 SIDE CHAIN PHOSPHORYLATED / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q53HS5, UniProt: P05107*PLUS #3: Water | ChemComp-HOH / | Compound details | ADAPTER PROTEIN IMPLICATED IN THE REGULATION OF A LARGE SPECTRUM OF BOTH GENERAL AND SPECIALIZED ...ADAPTER PROTEIN IMPLICATED | Sequence details | RESIDUES (-1-0) ARE REMNANTS OF A FUSION PROTEIN AND A PART OF ONLY THIS STRUCTURE | |
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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: 2.84 Å3/Da / Density % sol: 56.32 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: 18-19% PEG3350, 10MM CACL2, 1MM NICL2, 100MM TRIS PH8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 17, 2007 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→500.1 Å / Num. obs: 40994 / % possible obs: 99.9 % / Redundancy: 9 % / Biso Wilson estimate: 47 Å2 / Rmerge(I) obs: 0.096 / Rsym value: 0.09 / Net I/σ(I): 16.86 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 8.94 % / Rmerge(I) obs: 0.566 / Mean I/σ(I) obs: 4.91 / Rsym value: 0.534 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1A4O Resolution: 2.5→47.6 Å / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINTS / Cross valid method: THROUGHOUT / σ(F): 0 Stereochemistry target values: LEAST SQUARES RESIDUAL FOR HEMIHEDRAL TWINNING Details: USED TWINNING FRACTION 0.306. TWINNING OPERATOR H,-H-K,-L
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 80.04 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 65.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→47.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.59 Å / Total num. of bins used: 10
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Xplor file | Serial no: 1 / Param file: PROTEIN_REP_TPO4.PARAM / Topol file: PROTEIN_TPO3.TOP |