+Open data
-Basic information
Entry | Database: PDB / ID: 1mk7 | ||||||
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Title | CRYSTAL STRUCTURE OF AN INTEGRIN BETA3-TALIN CHIMERA | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / FOCAL ADHESION / INTEGRIN BINDING / FERM DOMAIN / CYTOSKELETON / NPXY MOTIF / PTB DOMAIN | ||||||
Function / homology | Function and homology information tube development / regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / alpha9-beta1 integrin-ADAM8 complex / regulation of trophoblast cell migration / regulation of postsynaptic neurotransmitter receptor diffusion trapping / alphav-beta3 integrin-vitronectin complex / maintenance of postsynaptic specialization structure / positive regulation of glomerular mesangial cell proliferation / regulation of extracellular matrix organization ...tube development / regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / alpha9-beta1 integrin-ADAM8 complex / regulation of trophoblast cell migration / regulation of postsynaptic neurotransmitter receptor diffusion trapping / alphav-beta3 integrin-vitronectin complex / maintenance of postsynaptic specialization structure / positive regulation of glomerular mesangial cell proliferation / regulation of extracellular matrix organization / platelet alpha granule membrane / integrin alphav-beta3 complex / negative regulation of lipoprotein metabolic process / alphav-beta3 integrin-PKCalpha complex / fibrinogen binding / glycinergic synapse / alphav-beta3 integrin-HMGB1 complex / vascular endothelial growth factor receptor 2 binding / blood coagulation, fibrin clot formation / negative regulation of lipid transport / negative regulation of low-density lipoprotein receptor activity / Elastic fibre formation / cell-substrate junction assembly / regulation of release of sequestered calcium ion into cytosol / mesodermal cell differentiation / alphav-beta3 integrin-IGF-1-IGF1R complex / angiogenesis involved in wound healing / platelet-derived growth factor receptor binding / filopodium membrane / extracellular matrix binding / positive regulation of fibroblast migration / positive regulation of vascular endothelial growth factor receptor signaling pathway / regulation of postsynaptic neurotransmitter receptor internalization / apolipoprotein A-I-mediated signaling pathway / regulation of bone resorption / wound healing, spreading of epidermal cells / apoptotic cell clearance / heterotypic cell-cell adhesion / integrin complex / positive regulation of cell adhesion mediated by integrin / Molecules associated with elastic fibres / cellular response to insulin-like growth factor stimulus / positive regulation of cell-matrix adhesion / cell adhesion mediated by integrin / smooth muscle cell migration / microvillus membrane / Syndecan interactions / negative chemotaxis / p130Cas linkage to MAPK signaling for integrins / cellular response to platelet-derived growth factor stimulus / protein disulfide isomerase activity / cell-substrate adhesion / positive regulation of smooth muscle cell migration / activation of protein kinase activity / positive regulation of osteoblast proliferation / TGF-beta receptor signaling activates SMADs / PECAM1 interactions / lamellipodium membrane / GRB2:SOS provides linkage to MAPK signaling for Integrins / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / platelet-derived growth factor receptor signaling pathway / fibronectin binding / ECM proteoglycans / positive regulation of T cell migration / positive regulation of bone resorption / Integrin cell surface interactions / coreceptor activity / negative regulation of endothelial cell apoptotic process / positive regulation of substrate adhesion-dependent cell spreading / embryo implantation / ruffle / positive regulation of endothelial cell proliferation / cell adhesion molecule binding / Integrin signaling / substrate adhesion-dependent cell spreading / cell-matrix adhesion / protein kinase C binding / positive regulation of endothelial cell migration / response to activity / Signal transduction by L1 / integrin-mediated signaling pathway / regulation of actin cytoskeleton organization / positive regulation of smooth muscle cell proliferation / Signaling by high-kinase activity BRAF mutants / wound healing / MAP2K and MAPK activation / structural constituent of cytoskeleton / cell-cell adhesion / platelet aggregation / ruffle membrane / platelet activation / VEGFA-VEGFR2 Pathway / cellular response to mechanical stimulus / positive regulation of angiogenesis / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / regulation of protein localization Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Garcia-Alvarez, B. / De Pereda, J.M. / Calderwood, D.A. / Ulmer, T.S. / Critchley, D. / Campbell, I.D. / Ginsberg, M.H. / Liddington, R.C. | ||||||
Citation | Journal: Mol.Cell / Year: 2003 Title: Structural Determinants of Integrin Recognition by Talin Authors: Garcia-Alvarez, B. / De Pereda, J.M. / Calderwood, D.A. / Ulmer, T.S. / Critchley, D. / Campbell, I.D. / Ginsberg, M.H. / Liddington, R.C. | ||||||
History |
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Remark 999 | SEQUENCE AUTHORS INFORMED THAT THE SEQUENCE OF CHICKEN TALIN IS NOT AVAILABLE IN ANY REFERENCE ...SEQUENCE AUTHORS INFORMED THAT THE SEQUENCE OF CHICKEN TALIN IS NOT AVAILABLE IN ANY REFERENCE DATABASE. THE SEQUENCE HAS BEEN DESCRIBED IN THE PUBLICATION: HEMMINGS, L., REES, D.J.G., OHANIAN, V., BOLTON, S.J., GILMORE, A.P., PATEL, N., PRIDDLE, H., TREVITHICK, J.E., HYNES, R.O., & CRITCHLEY, D.R. (1996). TALIN CONTAINS THREE ACTIN-BINDING SITES EACH OF WHICH IS ADJACENT TO A VINCULIN-BINDING SITE. J. CELL SCI., 109, 2715-2726. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mk7.cif.gz | 93.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mk7.ent.gz | 76.5 KB | Display | PDB format |
PDBx/mmJSON format | 1mk7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mk/1mk7 ftp://data.pdbj.org/pub/pdb/validation_reports/mk/1mk7 | HTTPS FTP |
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-Related structure data
Related structure data | 1mixSC 1mizC 1mk9C 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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Details | THE ASYMMETRIC UNIT CONTAINS TWO BIOLOGICAL HETERODIMERS OF INTEGRIN BETA3 AND TALIN. FIRST ONE IS FORMED BY CHAINS A AND D, AND THE SECOND BY CHAINS B AND C |
-Components
#1: Protein/peptide | Mass: 1764.912 Da / Num. of mol.: 2 / Fragment: PARTIAL CYTOPLASMIC TAIL (Residues 739-749) Source method: isolated from a genetically manipulated source Details: Forms chimera with talin at the N-terminus / Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P05106 #2: Protein | Mass: 22150.656 Da / Num. of mol.: 2 Fragment: F2 AND F3 SUBDOMAINS OF FERM DOMAIN (Residues 209-400) Source method: isolated from a genetically manipulated source Details: Forms chimera with Integrin Beta3 at the C-terminus Source: (gene. exp.) Gallus gallus (chicken) / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P54939 #3: 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: 2.63 Å3/Da / Density % sol: 53.15 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1 M TRIS-HCL, 18% (W/V) PEG-MME 2000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 4, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→29.89 Å / Num. obs: 21774 / % possible obs: 87 % / Observed criterion σ(I): -3 / Redundancy: 3.21 % / Biso Wilson estimate: 12.8 Å2 / Rsym value: 0.051 / Net I/σ(I): 23.8 |
Reflection shell | Resolution: 2.2→2.28 Å / Mean I/σ(I) obs: 5.1 / Rsym value: 0.199 / % possible all: 48.7 |
Reflection | *PLUS Highest resolution: 2.2 Å / Num. measured all: 68410 / Rmerge(I) obs: 0.051 |
Reflection shell | *PLUS % possible obs: 48.7 % / Rmerge(I) obs: 0.199 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1MIX Resolution: 2.2→29.89 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 32.3672 Å2 / ksol: 0.353863 e/Å3 | |||||||||||||||||||||
Displacement parameters | Biso mean: 25.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→29.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 30 Å / Rfactor Rfree: 0.25 | |||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||
Refine LS restraints | *PLUS
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