+Open data
-Basic information
Entry | Database: PDB / ID: 5ffo | |||||||||
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Title | Integrin alpha V beta 6 in complex with pro-TGF-beta | |||||||||
Components |
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Keywords | CELL ADHESION / Integrin / TGF-beta | |||||||||
Function / homology | Function and homology information positive regulation of primary miRNA processing / positive regulation of microglia differentiation / Influenza Virus Induced Apoptosis / negative regulation of skeletal muscle tissue development / TGFBR2 MSI Frameshift Mutants in Cancer / regulatory T cell differentiation / regulation of blood vessel remodeling / regulation of striated muscle tissue development / Langerhans cell differentiation / negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target ...positive regulation of primary miRNA processing / positive regulation of microglia differentiation / Influenza Virus Induced Apoptosis / negative regulation of skeletal muscle tissue development / TGFBR2 MSI Frameshift Mutants in Cancer / regulatory T cell differentiation / regulation of blood vessel remodeling / regulation of striated muscle tissue development / Langerhans cell differentiation / negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / regulation of protein import into nucleus / extracellular matrix assembly / embryonic liver development / type III transforming growth factor beta receptor binding / negative regulation of hyaluronan biosynthetic process / positive regulation of cardiac muscle cell differentiation / myofibroblast differentiation / connective tissue replacement involved in inflammatory response wound healing / odontoblast differentiation / negative regulation of macrophage cytokine production / integrin alphav-beta6 complex / integrin alphav-beta8 complex / hard palate development / transforming growth factor beta production / positive regulation of receptor signaling pathway via STAT / negative regulation of entry of bacterium into host cell / integrin alphav-beta5 complex / TGFBR2 Kinase Domain Mutants in Cancer / : / opsonin binding / positive regulation of isotype switching to IgA isotypes / positive regulation of mesenchymal stem cell proliferation / integrin alphav-beta1 complex / membrane protein intracellular domain proteolysis / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / heart valve morphogenesis / bronchiole development / Cross-presentation of particulate exogenous antigens (phagosomes) / enamel mineralization / extracellular matrix protein binding / positive regulation of vasculature development / hyaluronan catabolic process / regulation of transforming growth factor beta receptor signaling pathway / ATP biosynthetic process / Laminin interactions / receptor catabolic process / negative regulation of extracellular matrix disassembly / positive regulation of extracellular matrix assembly / integrin alphav-beta3 complex / negative regulation of lipoprotein metabolic process / type II transforming growth factor beta receptor binding / TGFBR1 LBD Mutants in Cancer / phospholipid homeostasis / alphav-beta3 integrin-PKCalpha complex / positive regulation of chemotaxis / entry into host cell by a symbiont-containing vacuole / negative regulation of biomineral tissue development / type I transforming growth factor beta receptor binding / alphav-beta3 integrin-HMGB1 complex / negative regulation of lipid transport / cell-cell junction organization / negative regulation of myoblast differentiation / negative regulation of low-density lipoprotein receptor activity / Elastic fibre formation / regulation of phagocytosis / positive regulation of vascular permeability / deubiquitinase activator activity / transforming growth factor beta binding / alphav-beta3 integrin-IGF-1-IGF1R complex / surfactant homeostasis / response to cholesterol / positive regulation of endothelial cell apoptotic process / positive regulation of small GTPase mediated signal transduction / filopodium membrane / extracellular matrix binding / positive regulation of chemokine (C-X-C motif) ligand 2 production / aortic valve morphogenesis / positive regulation of fibroblast migration / apolipoprotein A-I-mediated signaling pathway / phosphate-containing compound metabolic process / wound healing, spreading of epidermal cells / apoptotic cell clearance / negative regulation of protein localization to plasma membrane / heterotypic cell-cell adhesion / integrin complex / sprouting angiogenesis / neural tube development / Molecules associated with elastic fibres / RUNX3 regulates CDKN1A transcription / positive regulation of intracellular signal transduction / cell adhesion mediated by integrin / skin development / microvillus membrane / positive regulation of epidermal growth factor receptor signaling pathway / ventricular cardiac muscle tissue morphogenesis / macrophage derived foam cell differentiation / negative regulation of fat cell differentiation / Syndecan interactions / negative chemotaxis Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.49 Å | |||||||||
Authors | Dong, X. / Zhao, B. / Springer, T.A. | |||||||||
Citation | Journal: Nature / Year: 2017 Title: Force interacts with macromolecular structure in activation of TGF-beta. Authors: Dong, X. / Zhao, B. / Iacob, R.E. / Zhu, J. / Koksal, A.C. / Lu, C. / Engen, J.R. / Springer, T.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ffo.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5ffo.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 5ffo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ff/5ffo ftp://data.pdbj.org/pub/pdb/validation_reports/ff/5ffo | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 3 types, 8 molecules AEBFCDGH
#1: Protein | Mass: 65982.922 Da / Num. of mol.: 2 / Fragment: UNP residues 31-627 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ITGAV, MSK8, VNRA / Production host: Homo sapiens (human) / References: UniProt: P06756 #2: Protein | Mass: 28851.707 Da / Num. of mol.: 2 / Fragment: Unp residues 128-378 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ITGB6 / Production host: Homo sapiens (human) / References: UniProt: P18564 #3: Protein | Mass: 41489.371 Da / Num. of mol.: 4 / Fragment: UNP residues 34-390 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TGFB1, TGFB / Production host: Homo sapiens (human) / References: UniProt: P01137 |
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-Sugars , 8 types, 18 molecules
#4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Polysaccharide | Source method: isolated from a genetically manipulated source #7: Polysaccharide | Source method: isolated from a genetically manipulated source #8: Polysaccharide | Source method: isolated from a genetically manipulated source #9: Polysaccharide | Source method: isolated from a genetically manipulated source #10: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #12: Sugar | ChemComp-NAG / |
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-Non-polymers , 3 types, 19 molecules
#11: Chemical | ChemComp-CA / #13: Chemical | ChemComp-MN / #14: 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: 2.74 Å3/Da / Density % sol: 55.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 8% PEG8000 0.1M Immidazole / PH range: 7.5-8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03318 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jul 27, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03318 Å / Relative weight: 1 |
Reflection | Resolution: 3.49→50 Å / Num. obs: 45279 / % possible obs: 94.6 % / Redundancy: 1.8 % / CC1/2: 0.988 / Rmerge(I) obs: 0.168 / Net I/σ(I): 4.6 |
Reflection shell | Resolution: 3.5→3.64 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 0.4 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Resolution: 3.49→45.72 Å / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 27.95 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.49→45.72 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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