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Yorodumi- PDB-4mmx: Integrin AlphaVBeta3 ectodomain bound to the tenth domain of Fibr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4mmx | |||||||||
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Title | Integrin AlphaVBeta3 ectodomain bound to the tenth domain of Fibronectin | |||||||||
Components |
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Keywords | CELL ADHESION / integrin / A domain / hybrid domain / PSI / EGF repeats / beta TA thigh / beta propeller / RGD motif / fibronectin / vitronectin | |||||||||
Function / homology | Function and homology information integrin alphav-beta8 complex / integrin alphav-beta6 complex / transforming growth factor beta production / negative regulation of entry of bacterium into host cell / integrin alphav-beta5 complex / negative regulation of monocyte activation / opsonin binding / calcium-independent cell-matrix adhesion / negative regulation of transforming growth factor beta production / integrin alphav-beta1 complex ...integrin alphav-beta8 complex / integrin alphav-beta6 complex / transforming growth factor beta production / negative regulation of entry of bacterium into host cell / integrin alphav-beta5 complex / negative regulation of monocyte activation / opsonin binding / calcium-independent cell-matrix adhesion / negative regulation of transforming growth factor beta production / integrin alphav-beta1 complex / Fibronectin matrix formation / Cross-presentation of particulate exogenous antigens (phagosomes) / Extracellular matrix organization / positive regulation of substrate-dependent cell migration, cell attachment to substrate / extracellular matrix protein binding / 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 / integrin alphaIIb-beta3 complex / neural crest cell migration involved in autonomic nervous system development / regulation of postsynaptic neurotransmitter receptor diffusion trapping / peptidase activator activity / alphav-beta3 integrin-vitronectin complex / fibrinogen complex / Laminin interactions / regulation of extracellular matrix organization / platelet alpha granule membrane / positive regulation of glomerular mesangial cell proliferation / negative regulation of lipoprotein metabolic process / integrin alphav-beta3 complex / negative regulation of low-density lipoprotein receptor activity / peptide cross-linking / fibrinogen binding / alphav-beta3 integrin-PKCalpha complex / maintenance of postsynaptic specialization structure / alphav-beta3 integrin-HMGB1 complex / regulation of phagocytosis / blood coagulation, fibrin clot formation / mesodermal cell differentiation / vascular endothelial growth factor receptor 2 binding / negative regulation of lipid transport / integrin activation / glycinergic synapse / ALK mutants bind TKIs / angiogenesis involved in wound healing / Elastic fibre formation / regulation of release of sequestered calcium ion into cytosol / alphav-beta3 integrin-IGF-1-IGF1R complex / cell-substrate junction assembly / transforming growth factor beta binding / platelet-derived growth factor receptor binding / entry into host cell by a symbiont-containing vacuole / positive regulation of small GTPase mediated signal transduction / filopodium membrane / extracellular matrix binding / positive regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of fibroblast migration / regulation of postsynaptic neurotransmitter receptor internalization / apolipoprotein A-I-mediated signaling pathway / regulation of bone resorption / apoptotic cell clearance / positive regulation of cell adhesion mediated by integrin / wound healing, spreading of epidermal cells / heterotypic cell-cell adhesion / integrin complex / biological process involved in interaction with symbiont / proteoglycan binding / positive regulation of intracellular signal transduction / Molecules associated with elastic fibres / extracellular matrix structural constituent / smooth muscle cell migration / cell adhesion mediated by integrin / positive regulation of cell-matrix adhesion / MET activates PTK2 signaling / microvillus membrane / negative chemotaxis / Syndecan interactions / cellular response to insulin-like growth factor stimulus / activation of protein kinase activity / p130Cas linkage to MAPK signaling for integrins / cell-substrate adhesion / protein disulfide isomerase activity / positive regulation of smooth muscle cell migration / endodermal cell differentiation / positive regulation of osteoblast proliferation / cellular response to platelet-derived growth factor stimulus / TGF-beta receptor signaling activates SMADs / PECAM1 interactions / GRB2:SOS provides linkage to MAPK signaling for Integrins / endoplasmic reticulum-Golgi intermediate compartment / lamellipodium membrane / platelet-derived growth factor receptor signaling pathway / fibronectin binding / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / Non-integrin membrane-ECM interactions / basement membrane / ECM proteoglycans Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.32 Å | |||||||||
Authors | van Agthoven, J. / Xiong, J. / Arnaout, M.A. | |||||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2014 Title: Structural basis for pure antagonism of integrin alpha V beta 3 by a high-affinity form of fibronectin. Authors: Van Agthoven, J.F. / Xiong, J.P. / Alonso, J.L. / Rui, X. / Adair, B.D. / Goodman, S.L. / Arnaout, M.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mmx.cif.gz | 696.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mmx.ent.gz | 585.6 KB | Display | PDB format |
PDBx/mmJSON format | 4mmx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4mmx_validation.pdf.gz | 2.8 MB | Display | wwPDB validaton report |
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Full document | 4mmx_full_validation.pdf.gz | 2.9 MB | Display | |
Data in XML | 4mmx_validation.xml.gz | 62.9 KB | Display | |
Data in CIF | 4mmx_validation.cif.gz | 82.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mm/4mmx ftp://data.pdbj.org/pub/pdb/validation_reports/mm/4mmx | HTTPS FTP |
-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, 3 molecules ABC
#1: Protein | Mass: 106048.359 Da / Num. of mol.: 1 / Fragment: Extracellular domain (UNP residues 31-989) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: alphav, ITGAV, MSK8, VNRA / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Hi5 / References: UniProt: P06756 |
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#2: Protein | Mass: 76523.125 Da / Num. of mol.: 1 / Fragment: Extracellular domain (UNP residues 27-718) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GP3A, ITGB3 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Hi5 / References: UniProt: P05106 |
#3: Protein | Mass: 10349.573 Da / Num. of mol.: 1 Fragment: Fibronectin type-III domain 10 (UNP residues 1448-1540) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: Fibronectin, FN, FN1 / Plasmid: pET / Production host: Escherichia coli (E. coli) / References: UniProt: P02751 |
-Sugars , 5 types, 14 molecules
#4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #6: Polysaccharide | alpha-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]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 #7: Polysaccharide | Source method: isolated from a genetically manipulated source #8: Sugar | ChemComp-NAG / |
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-Non-polymers , 2 types, 10 molecules
#9: Chemical | ChemComp-MN / #10: 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: 3.85 Å3/Da / Density % sol: 68.05 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 12% PEG3350, 0.8 M sodium chloride, 0.1 M sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 13, 2012 |
Radiation | Monochromator: sagitally focused Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97921 Å / Relative weight: 1 |
Reflection | Resolution: 3.32→75.49 Å / Num. all: 67157 / Num. obs: 39593 / % possible obs: 88 % / Observed criterion σ(F): 5.3 / Observed criterion σ(I): 5.3 / Redundancy: 6.2 % / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 3.32→3.41 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 3.3 / Rsym value: 0.676 / % possible all: 88 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.32→42.506 Å / SU ML: 0.42 / σ(F): 1.38 / Phase error: 25.86 / Stereochemistry target values: ML
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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: 3.32→42.506 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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