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Yorodumi- PDB-1m1x: CRYSTAL STRUCTURE OF THE EXTRACELLULAR SEGMENT OF INTEGRIN ALPHA ... -
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-Basic information
Entry | Database: PDB / ID: 1m1x | |||||||||
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Title | CRYSTAL STRUCTURE OF THE EXTRACELLULAR SEGMENT OF INTEGRIN ALPHA VBETA3 BOUND TO MN2+ | |||||||||
Components |
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Keywords | CELL ADHESION / GENU / HYBRID DOMAIN / BETA-TAIL DOMAIN / PSI DOMAIN / EGF DOMAIN / MIDAS / ADMIDAS / CAGE MOTIF / PROPELLER / A-DOMAIN / THIGH DOMAIN / CALF DOMAIN | |||||||||
Function / homology | Function and homology information integrin alphav-beta6 complex / integrin alphav-beta8 complex / transforming growth factor beta production / negative regulation of entry of bacterium into host cell / integrin alphav-beta5 complex / : / opsonin binding / integrin alphav-beta1 complex / Cross-presentation of particulate exogenous antigens (phagosomes) / extracellular matrix protein binding ...integrin alphav-beta6 complex / integrin alphav-beta8 complex / transforming growth factor beta production / negative regulation of entry of bacterium into host cell / integrin alphav-beta5 complex / : / opsonin binding / integrin alphav-beta1 complex / Cross-presentation of particulate exogenous antigens (phagosomes) / 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 / regulation of postsynaptic neurotransmitter receptor diffusion trapping / alphav-beta3 integrin-vitronectin complex / regulation of extracellular matrix organization / Laminin interactions / platelet alpha granule membrane / positive regulation of glomerular mesangial cell proliferation / integrin alphav-beta3 complex / negative regulation of lipoprotein metabolic process / alphav-beta3 integrin-PKCalpha complex / entry into host cell by a symbiont-containing vacuole / fibrinogen binding / maintenance of postsynaptic specialization structure / alphav-beta3 integrin-HMGB1 complex / blood coagulation, fibrin clot formation / negative regulation of lipid transport / vascular endothelial growth factor receptor 2 binding / glycinergic synapse / negative regulation of low-density lipoprotein receptor activity / angiogenesis involved in wound healing / regulation of phagocytosis / Elastic fibre formation / regulation of release of sequestered calcium ion into cytosol / mesodermal cell differentiation / cell-substrate junction assembly / alphav-beta3 integrin-IGF-1-IGF1R complex / transforming growth factor beta binding / platelet-derived growth factor receptor binding / filopodium membrane / positive regulation of small GTPase mediated signal transduction / extracellular matrix binding / regulation of postsynaptic neurotransmitter receptor internalization / positive regulation of fibroblast migration / positive regulation of vascular endothelial growth factor receptor signaling pathway / 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 / Molecules associated with elastic fibres / positive regulation of intracellular signal transduction / positive regulation of cell-matrix adhesion / cellular response to insulin-like growth factor stimulus / smooth muscle cell migration / microvillus membrane / negative chemotaxis / cell adhesion mediated by integrin / Syndecan interactions / p130Cas linkage to MAPK signaling for integrins / activation of protein kinase activity / cellular response to platelet-derived growth factor stimulus / cell-substrate adhesion / protein disulfide isomerase activity / positive regulation of smooth muscle cell migration / endodermal cell differentiation / 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 / platelet-derived growth factor receptor signaling pathway / negative regulation of lipid storage / fibronectin binding / positive regulation of cell adhesion / ECM proteoglycans / voltage-gated calcium channel activity / positive regulation of T cell migration / positive regulation of bone resorption / vasculogenesis / Integrin cell surface interactions / coreceptor activity / specific granule membrane / negative regulation of endothelial cell apoptotic process / positive regulation of substrate adhesion-dependent cell spreading / extrinsic apoptotic signaling pathway in absence of ligand / cell adhesion molecule binding / positive regulation of endothelial cell proliferation / ERK1 and ERK2 cascade / embryo implantation / phagocytic vesicle / positive regulation of endothelial cell migration / Integrin signaling / substrate adhesion-dependent cell spreading Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.3 Å | |||||||||
Authors | Xiong, J.-P. / Stehle, T. / Zhang, R. / Joachimiak, A. / Frech, M. / Goodman, S.L. / Arnaout, M.A. | |||||||||
Citation | Journal: Science / Year: 2002 Title: Crystal structure of the extracellular segment of integrin alpha Vbeta3 in complex with an Arg-Gly-Asp ligand. Authors: Xiong, J.P. / Stehle, T. / Zhang, R. / Joachimiak, A. / Frech, M. / 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 | 1m1x.cif.gz | 299.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m1x.ent.gz | 241.1 KB | Display | PDB format |
PDBx/mmJSON format | 1m1x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1m1x_validation.pdf.gz | 807.2 KB | Display | wwPDB validaton report |
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Full document | 1m1x_full_validation.pdf.gz | 880.9 KB | Display | |
Data in XML | 1m1x_validation.xml.gz | 39.1 KB | Display | |
Data in CIF | 1m1x_validation.cif.gz | 56.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m1/1m1x ftp://data.pdbj.org/pub/pdb/validation_reports/m1/1m1x | 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 , 2 types, 2 molecules AB
#1: Protein | Mass: 105880.164 Da / Num. of mol.: 1 / Fragment: RESIDUES 31-987 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line: SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: GenBank: 14743192, UniProt: P06756*PLUS |
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#2: Protein | Mass: 76650.305 Da / Num. of mol.: 1 / Fragment: RESIDUES 27-718 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line: SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P05106 |
-Sugars , 3 types, 11 molecules
#3: 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 #4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-NAG / |
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-Non-polymers , 1 types, 6 molecules
#6: Chemical | ChemComp-MN / |
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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: 4.17 Å3/Da / Density % sol: 70.51 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG, MES, Mn, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 278K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0332 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Jun 24, 2001 |
Radiation | Monochromator: UNDULATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→50 Å / Num. all: 47393 / Num. obs: 44739 / % possible obs: 94.4 % / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 3.3→3.4 Å / % possible all: 86.1 |
-Processing
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 3.3→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 3.3→20 Å
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Refine LS restraints |
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