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- PDB-2v7d: 14-3-3 protein zeta in complex with Thr758 phosphorylated integri... -
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Open data
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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 | ||||||
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![]() | 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 | ![]() 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 / integrin alphaX-beta2 complex / : / cellular extravasation / GP1b-IX-V activation signalling ...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 / integrin alphaX-beta2 complex / : / cellular extravasation / GP1b-IX-V activation signalling / positive regulation of prostaglandin-E synthase activity / positive regulation of neutrophil degranulation / integrin alphaM-beta2 complex / integrin alphaL-beta2 complex / ICAM-3 receptor activity / Deactivation of the beta-catenin transactivating complex / neutrophil degranulation / : / Rap1 signalling / TP53 Regulates Metabolic Genes / complement component C3b binding / Interleukin-3, Interleukin-5 and GM-CSF signaling / neutrophil migration / Toll Like Receptor 4 (TLR4) Cascade / negative regulation of dopamine metabolic process / leukocyte migration involved in inflammatory response / cell-cell adhesion via plasma-membrane adhesion molecules / natural killer cell activation / heterotypic cell-cell adhesion / integrin complex / positive regulation of leukocyte adhesion to vascular endothelial cell / toll-like receptor 4 signaling pathway / cell adhesion mediated by integrin / leukocyte cell-cell adhesion / phagocytosis, engulfment / leukocyte migration / amyloid-beta clearance / endodermal cell differentiation / receptor clustering / plasma membrane raft / tertiary granule membrane / ficolin-1-rich granule membrane / cellular response to low-density lipoprotein particle stimulus / phosphoserine residue binding / regulation of immune response / endothelial cell migration / positive regulation of protein targeting to membrane / Integrin cell surface interactions / specific granule membrane / regulation of peptidyl-tyrosine phosphorylation / cell adhesion molecule binding / heat shock protein binding / protein sequestering activity / extracellular matrix organization / neutrophil chemotaxis / regulation of ERK1 and ERK2 cascade / cell-matrix adhesion / receptor-mediated endocytosis / positive regulation of superoxide anion generation / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / microglial cell activation / receptor internalization / cytokine-mediated signaling pathway / cell-cell adhesion / positive regulation of angiogenesis / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of nitric oxide biosynthetic process / extracellular vesicle / melanosome / cell migration / integrin binding / cell-cell signaling / positive regulation of NF-kappaB transcription factor activity / amyloid-beta binding / regulation of cell shape / Interleukin-4 and Interleukin-13 signaling / receptor complex / cell adhesion / inflammatory response / external side of plasma membrane / protein phosphorylation / focal adhesion / apoptotic process / Neutrophil degranulation / protein kinase binding / cell surface / signal transduction / extracellular exosome / membrane / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Takala, H. / Ylanne, J. | ||||||
![]() | ![]() 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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 195.3 KB | Display | ![]() |
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PDB format | ![]() | 157.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 488.9 KB | Display | ![]() |
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Full document | ![]() | 540.2 KB | Display | |
Data in XML | ![]() | 41 KB | Display | |
Data in CIF | ![]() | 55.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2jf1C ![]() 1a4oS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() ![]() #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.) ![]() #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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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 |