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- PDB-2vdr: Integrin AlphaIIbBeta3 Headpiece Bound to a chimeric Fibrinogen G... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2vdr | |||||||||
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Title | Integrin AlphaIIbBeta3 Headpiece Bound to a chimeric Fibrinogen Gamma chain peptide, LGGAKQRGDV | |||||||||
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![]() | 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 | ![]() 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 / fibrinogen complex / integrin alphaIIb-beta3 complex / regulation of postsynaptic neurotransmitter receptor diffusion trapping / maintenance of postsynaptic specialization structure ...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 / fibrinogen complex / integrin alphaIIb-beta3 complex / regulation of postsynaptic neurotransmitter receptor diffusion trapping / maintenance of postsynaptic specialization structure / alphav-beta3 integrin-vitronectin complex / regulation of extracellular matrix organization / positive regulation of glomerular mesangial cell proliferation / Regulation of TLR by endogenous ligand / platelet alpha granule / platelet alpha granule membrane / integrin alphav-beta3 complex / negative regulation of lipoprotein metabolic process / alphav-beta3 integrin-PKCalpha complex / fibrinogen binding / blood coagulation, fibrin clot formation / alphav-beta3 integrin-HMGB1 complex / vascular endothelial growth factor receptor 2 binding / negative regulation of lipid transport / positive regulation of vascular endothelial growth factor signaling pathway / regulation of release of sequestered calcium ion into cytosol / Elastic fibre formation / glycinergic synapse / mesodermal cell differentiation / cell-substrate junction assembly / alphav-beta3 integrin-IGF-1-IGF1R complex / platelet-derived growth factor receptor binding / positive regulation of heterotypic cell-cell adhesion / MyD88 deficiency (TLR2/4) / filopodium membrane / extracellular matrix binding / angiogenesis involved in wound healing / positive regulation of vascular endothelial growth factor receptor signaling pathway / regulation of bone resorption / apolipoprotein A-I-mediated signaling pathway / positive regulation of cell adhesion mediated by integrin / positive regulation of leukocyte migration / apoptotic cell clearance / integrin complex / wound healing, spreading of epidermal cells / heterotypic cell-cell adhesion / positive regulation of fibroblast migration / IRAK4 deficiency (TLR2/4) / extracellular matrix structural constituent / positive regulation of smooth muscle cell migration / smooth muscle cell migration / Molecules associated with elastic fibres / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / plasminogen activation / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / positive regulation of cell-matrix adhesion / negative chemotaxis / cellular response to insulin-like growth factor stimulus / cell adhesion mediated by integrin / Syndecan interactions / p130Cas linkage to MAPK signaling for integrins / positive regulation of osteoblast proliferation / microvillus membrane / regulation of postsynaptic neurotransmitter receptor internalization / protein disulfide isomerase activity / positive regulation of peptide hormone secretion / cell-substrate adhesion / platelet-derived growth factor receptor signaling pathway / PECAM1 interactions / TGF-beta receptor signaling activates SMADs / GRB2:SOS provides linkage to MAPK signaling for Integrins / lamellipodium membrane / positive regulation of exocytosis / fibronectin binding / positive regulation of bone resorption / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / protein secretion / protein polymerization / ECM proteoglycans / Integrin cell surface interactions / positive regulation of T cell migration / Common Pathway of Fibrin Clot Formation / negative regulation of endothelial cell apoptotic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of vasoconstriction / coreceptor activity / fibrinolysis / cellular response to platelet-derived growth factor stimulus / cell adhesion molecule binding / positive regulation of endothelial cell proliferation / Integrin signaling / positive regulation of substrate adhesion-dependent cell spreading / embryo implantation / positive regulation of endothelial cell migration / substrate adhesion-dependent cell spreading / protein kinase C binding / platelet alpha granule lumen / cell-matrix adhesion / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Springer, T.A. / Zhu, J. / Xiao, T. | |||||||||
![]() | ![]() Title: Structural Basis for Distinctive Recognition of Fibrinogen Gammac Peptide by the Platelet Integrin Alphaiibbeta3. Authors: Springer, T.A. / Zhu, J. / Xiao, T. #1: ![]() 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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 314.7 KB | Display | ![]() |
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PDB format | ![]() | 250.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 714.6 KB | Display | ![]() |
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Full document | ![]() | 728.8 KB | Display | |
Data in XML | ![]() | 70.2 KB | Display | |
Data in CIF | ![]() | 98.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2vc2C ![]() 2vdkC ![]() 2vdlC ![]() 2vdmC ![]() 2vdnC ![]() 2vdoC ![]() 2vdpC ![]() 2vdqC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() |
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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.) ![]() ![]() ![]() |
-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.) ![]() |
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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) ![]() ![]() |
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#5: Antibody | Mass: 23332.686 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-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 | ENGINEEREDHas protein modification | Y | Sequence 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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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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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