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Yorodumi- PDB-2vdr: Integrin AlphaIIbBeta3 Headpiece Bound to a chimeric Fibrinogen G... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vdr | |||||||||
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Title | Integrin AlphaIIbBeta3 Headpiece Bound to a chimeric Fibrinogen Gamma chain peptide, LGGAKQRGDV | |||||||||
Components |
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Keywords | CELL ADHESION/IMMUNE SYSTEM / CELL ADHESION-IMMUNE SYSTEM COMPLEX / FIBRINOGEN BINDING / PLATELET INTEGRIN ALPHAIIBBETA3 / GLYCOPROTEIN / CELL ADHESION / MEMBRANE / INTEGRIN / RECEPTOR / ANTAGONIST / HOST-VIRUS INTERACTION / PYRROLIDONE CARBOXYLIC ACID / TRANSMEMBRANE / PHOSPHORYLATION / DISEASE MUTATION / CLEAVAGE ON PAIR OF BASIC RESIDUES | |||||||||
Function / homology | Function and homology information platelet maturation / 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 ...platelet maturation / 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 / fibrinogen complex / integrin alphav-beta3 complex / negative regulation of lipoprotein metabolic process / Regulation of TLR by endogenous ligand / 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 / platelet alpha granule / 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 / cellular response to interleukin-6 / platelet-derived growth factor receptor binding / filopodium membrane / extracellular matrix binding / MyD88 deficiency (TLR2/4) / 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 / wound healing, spreading of epidermal cells / 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 heterotypic cell-cell adhesion / cellular response to insulin-like growth factor stimulus / IRAK4 deficiency (TLR2/4) / positive regulation of leukocyte migration / positive regulation of cell-matrix adhesion / cell adhesion mediated by integrin / smooth muscle cell migration / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / microvillus membrane / extracellular matrix structural constituent / Syndecan interactions / negative chemotaxis / plasminogen activation / 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 / positive regulation of peptide hormone secretion / activation of protein kinase activity / positive regulation of exocytosis / 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 / protein secretion / protein polymerization / ECM proteoglycans / positive regulation of bone resorption / positive regulation of T cell migration / cellular response to interleukin-1 / Integrin cell surface interactions / coreceptor activity / negative regulation of endothelial cell apoptotic process / Common Pathway of Fibrin Clot Formation / positive regulation of substrate adhesion-dependent cell spreading / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of vasoconstriction / embryo implantation / fibrinolysis / positive regulation of endothelial cell proliferation / cell adhesion molecule binding / cell-matrix adhesion / Integrin signaling / substrate adhesion-dependent cell spreading / protein kinase C binding / response to activity / positive regulation of endothelial cell migration Similarity search - Function | |||||||||
Biological species | HOMO SAPIENS (human) MUS MUSCULUS (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.4 Å | |||||||||
Authors | Springer, T.A. / Zhu, J. / Xiao, T. | |||||||||
Citation | Journal: J.Cell Biol. / Year: 2008 Title: Structural Basis for Distinctive Recognition of Fibrinogen Gammac Peptide by the Platelet Integrin Alphaiibbeta3. Authors: Springer, T.A. / Zhu, J. / Xiao, T. #1: Journal: Nature / Year: 2004 Title: Structural Basis for Allostery in Integrins and Binding to Fibrinogen-Mimetic Therapeutics Authors: Xiao, T. / Takagi, J. / Coller, B.S. / Wang, J.-H. / Springer, T.A. | |||||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vdr.cif.gz | 309.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vdr.ent.gz | 250.8 KB | Display | PDB format |
PDBx/mmJSON format | 2vdr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vd/2vdr ftp://data.pdbj.org/pub/pdb/validation_reports/vd/2vdr | HTTPS FTP |
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-Related structure data
Related structure data | 2vc2C 2vdkC 2vdlC 2vdmC 2vdnC 2vdoC 2vdpC 2vdqC 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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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 49030.367 Da / Num. of mol.: 1 / Fragment: HEADPIECE, RESIDUES 32-483 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): LEC 3.2.8.1 / Production host: CRICETULUS GRISEUS (Chinese hamster) / References: UniProt: P08514 |
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#2: Protein | Mass: 50969.664 Da / Num. of mol.: 1 / Fragment: HEADPIECE, RESIDUES 27-487 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): LEC 3.2.8.1 / Production host: CRICETULUS GRISEUS (Chinese hamster) / References: UniProt: P05106 |
-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | Mass: 1002.127 Da / Num. of mol.: 1 / Fragment: GAMMA CHAIN C-TERMINAL PEPTIDE, RESIDUES 428-437 / Mutation: YES / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q53Y18, UniProt: P02679*PLUS |
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-Antibody , 2 types, 2 molecules HL
#4: Antibody | Mass: 23766.473 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) / Cell line: 10E5 HYBRIDOMA / Strain: BALB/C |
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#5: Antibody | Mass: 23332.686 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) / Cell line: 10E5 HYBRIDOMA / Strain: BALB/C |
-Sugars , 3 types, 5 molecules
#6: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-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 |
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#7: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-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 |
#10: Sugar |
-Non-polymers , 4 types, 1151 molecules
#8: Chemical | #9: Chemical | ChemComp-CA / #11: Chemical | ChemComp-MG / | #12: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEEREDSequence details | ACCORDING TO THE AUTHORS THE CORRECT CHAIN A SEQUENCE IS ANNOTATED IN NCBI ENTRY GI 88758615 WHICH ...ACCORDING TO THE AUTHORS THE CORRECT CHAIN A SEQUENCE IS ANNOTATED IN NCBI ENTRY GI 88758615 WHICH SHOULD BE USED IN PLACE OF P08514. THERE IS A A408R MUTATION ACCORDING TO THE AUTHORS THE CORRECT CHAIN C SEQUENCE IS ANNOTATED IN NCBI ENTRY GI 70906437 WHICH CORRESPOND | |
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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: 3.8 Å3/Da / Density % sol: 67.2 % / Description: NONE |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 11% PEG 3350, 0.7 M MAGNESIUM ACETATE, 0.1 M SODIUM CACODYLATE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.07223 |
Detector | Type: CUSTOM (SBC2 3K) / Detector: CCD / Date: Dec 15, 2004 / Details: MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07223 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 609049 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 2.4→2.5 Å / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.3 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 2.4→43.44 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.949 / SU B: 9.822 / SU ML: 0.127 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.22 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.58 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→43.44 Å
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