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Yorodumi- PDB-3nig: The Closed Headpiece of Integrin IIb 3 and its Complex with an II... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3nig | |||||||||
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Title | The Closed Headpiece of Integrin IIb 3 and its Complex with an IIb 3 -Specific Antagonist That Does Not Induce Opening | |||||||||
Components |
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Keywords | CELL ADHESION/BLOOD CLOTTING / integrin / headpiece / alphaIIB / beta3 / CELL ADHESION-IMMUNE SYSTEM complex / CELL ADHESION-BLOOD CLOTTING complex | |||||||||
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 / apoptotic cell clearance / heterotypic cell-cell adhesion / integrin complex / positive regulation of cell adhesion mediated by integrin / Molecules associated with elastic fibres / positive regulation of leukocyte migration / 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 / TGF-beta receptor signaling activates SMADs / positive regulation of osteoblast proliferation / 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 / positive regulation of endothelial cell proliferation / cell adhesion molecule binding / cell-matrix adhesion / Integrin signaling / substrate adhesion-dependent cell spreading / response to activity / positive regulation of endothelial cell migration / Signal transduction by L1 / integrin-mediated signaling pathway / protein kinase C binding / regulation of actin cytoskeleton organization / positive regulation of smooth muscle cell proliferation / Signaling by high-kinase activity BRAF mutants / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / MAP2K and MAPK activation / wound healing / cell-cell adhesion / platelet aggregation / platelet activation / VEGFA-VEGFR2 Pathway / ruffle membrane / cellular response to mechanical stimulus / Signaling by RAF1 mutants / positive regulation of angiogenesis / 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 / positive regulation of fibroblast proliferation Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | |||||||||
Authors | Zhu, J.H. / Zhu, J.Q. / Springer, T.A. | |||||||||
Citation | Journal: Blood / Year: 2010 Title: Closed headpiece of integrin {alpha}IIb{beta}3 and its complex with an {alpha}IIb{beta}3-specific antagonist that does not induce opening. Authors: Zhu, J. / Zhu, J. / Negri, A. / Provasi, D. / Filizola, M. / Coller, B.S. / 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 | 3nig.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb3nig.ent.gz | 898.7 KB | Display | PDB format |
PDBx/mmJSON format | 3nig.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ni/3nig ftp://data.pdbj.org/pub/pdb/validation_reports/ni/3nig | HTTPS FTP |
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-Related structure data
Related structure data | 3nidSC 3nifC 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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2 |
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Unit cell |
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-Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 49515.965 Da / Num. of mol.: 2 / Fragment: Integrin alpha-IIb, residues 32-488 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ITGA2B, GP2B, ITGAB / Plasmid: pCDNA 3.1, pEF1 / Cell (production host): CHO / Cell line (production host): Lec 3.2.8.1 / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): CHO Lec 3.2.8.1 / References: UniProt: P08514 #2: Protein | Mass: 51958.789 Da / Num. of mol.: 2 / Fragment: Integrin beta-3, residues 27-497 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ITGB3, GP3A / Plasmid: pCDNA 3.1, pEF1 / Cell (production host): CHO / Cell line (production host): Lec 3.2.8.1 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P05106 |
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-Antibody , 2 types, 4 molecules EHFL
#3: Antibody | Mass: 23766.473 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB/C / Cell line: 10E5 HYBRIDOMA #4: Antibody | Mass: 23332.686 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB/C / Cell line: 10E5 HYBRIDOMA |
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-Sugars , 3 types, 6 molecules
#5: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Polysaccharide | Source method: isolated from a genetically manipulated source #11: Sugar | |
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-Non-polymers , 5 types, 1250 molecules
#7: Chemical | ChemComp-CA / #8: Chemical | #9: Chemical | ChemComp-SO4 / #10: Chemical | #12: 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: 3.33 Å3/Da / Density % sol: 63.01 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.9 Details: 11% PEG 8000, 0.2 M ammonium sulfate, 0.1 M Tris-HCl, pH 8.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97948 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 14, 2009 |
Radiation | Monochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97948 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→50 Å / Num. all: 187880 / Num. obs: 187671 / % possible obs: 99.9 % / Redundancy: 6.63 % / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 12.11 |
Reflection shell | Resolution: 2.25→2.31 Å / Redundancy: 5.98 % / Rmerge(I) obs: 0.994 / Mean I/σ(I) obs: 1.9 / Num. unique all: 13781 / % possible all: 99.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3NID Resolution: 2.25→48.491 Å / SU ML: 0.33 / σ(F): 1.99 / 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 / Bsol: 44.268 Å2 / ksol: 0.378 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.25→48.491 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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