+Open data
-Basic information
Entry | Database: PDB / ID: 2vdl | ||||||||||||
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Title | Re-refinement of Integrin AlphaIIbBeta3 Headpiece | ||||||||||||
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 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 / regulation of postsynaptic neurotransmitter receptor diffusion trapping / alphav-beta3 integrin-vitronectin complex / regulation of extracellular matrix organization / platelet alpha granule membrane ...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 / regulation of postsynaptic neurotransmitter receptor diffusion trapping / alphav-beta3 integrin-vitronectin complex / regulation of extracellular matrix organization / 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 / fibrinogen binding / maintenance of postsynaptic specialization structure / alphav-beta3 integrin-HMGB1 complex / blood coagulation, fibrin clot formation / vascular endothelial growth factor receptor 2 binding / negative regulation of lipid transport / glycinergic synapse / negative regulation of low-density lipoprotein receptor activity / angiogenesis involved in wound healing / 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 / platelet-derived growth factor receptor binding / filopodium membrane / extracellular matrix binding / positive regulation of fibroblast migration / regulation of postsynaptic neurotransmitter receptor internalization / positive regulation of vascular endothelial growth factor receptor signaling pathway / apolipoprotein A-I-mediated signaling pathway / regulation of bone resorption / apoptotic cell clearance / negative regulation of macrophage derived foam cell differentiation / positive regulation of cell adhesion mediated by integrin / wound healing, spreading of epidermal cells / heterotypic cell-cell adhesion / negative regulation of lipid storage / integrin complex / Molecules associated with elastic fibres / positive regulation of leukocyte migration / cellular response to insulin-like growth factor stimulus / positive regulation of cell-matrix adhesion / smooth muscle cell migration / cell adhesion mediated by integrin / microvillus membrane / positive regulation of bone resorption / negative chemotaxis / Syndecan interactions / p130Cas linkage to MAPK signaling for integrins / cellular response to platelet-derived growth factor stimulus / activation of protein kinase activity / cell-substrate adhesion / protein disulfide isomerase activity / positive regulation of smooth muscle cell migration / positive regulation of osteoblast proliferation / TGF-beta receptor signaling activates SMADs / PECAM1 interactions / lamellipodium membrane / GRB2:SOS provides linkage to MAPK signaling for Integrins / platelet-derived growth factor receptor signaling pathway / fibronectin binding / ECM proteoglycans / positive regulation of T cell migration / Integrin cell surface interactions / coreceptor activity / negative regulation of endothelial cell apoptotic process / positive regulation of substrate adhesion-dependent cell spreading / Signal transduction by L1 / cell adhesion molecule binding / positive regulation of endothelial cell proliferation / embryo implantation / positive regulation of endothelial cell migration / Integrin signaling / substrate adhesion-dependent cell spreading / positive regulation of smooth muscle cell proliferation / cell-matrix adhesion / response to activity / integrin-mediated signaling pathway / regulation of actin cytoskeleton organization / protein kinase C binding / cell-cell adhesion / ruffle membrane / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / wound healing / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / cellular response to mechanical stimulus / platelet activation / platelet aggregation / VEGFA-VEGFR2 Pathway / positive regulation of fibroblast proliferation / integrin binding / cellular response to xenobiotic stimulus / positive regulation of angiogenesis / Signaling by RAF1 mutants Similarity search - Function | ||||||||||||
Biological species | HOMO SAPIENS (human) MUS MUSCULUS (house mouse) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 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 | 2vdl.cif.gz | 313.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vdl.ent.gz | 250.4 KB | Display | PDB format |
PDBx/mmJSON format | 2vdl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vdl_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 2vdl_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 2vdl_validation.xml.gz | 27.7 KB | Display | |
Data in CIF | 2vdl_validation.cif.gz | 48.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vd/2vdl ftp://data.pdbj.org/pub/pdb/validation_reports/vd/2vdl | HTTPS FTP |
-Related structure data
Related structure data | 2vc2C 2vdkC 2vdmC 2vdnC 2vdoC 2vdpC 2vdqC 2vdrC 1jv2S C: citing same article (ref.) S: Starting model for refinement |
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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 |
-Antibody , 2 types, 2 molecules HL
#3: 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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#4: 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
#5: 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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#6: 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 |
#9: Sugar |
-Non-polymers , 5 types, 1139 molecules
#7: Chemical | #8: Chemical | ChemComp-CA / #10: Chemical | ChemComp-CAC / | #11: Chemical | ChemComp-MG / | #12: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | CACODYLATE ION (CAC): CACODYLATE IS FOUND IN THE LIGAND BINDING SITE. BASED ON IMPURITIES IN ...CACODYLATE |
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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. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.7 Å3/Da / Density % sol: 66.8 % / Description: NONE |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 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: 0.9793 |
Detector | Type: CUSTOM (SBC2 3K) / Detector: CCD / Date: Aug 5, 2003 / Details: MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→50 Å / Num. obs: 62512 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2.75→2.85 Å / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JV2 Resolution: 2.75→42.99 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.936 / SU B: 15.066 / SU ML: 0.167 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.562 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THESE ARE RE-REFINED COORDINATES OF THE PREVIOUS WWPDB SUBMISSION 1TXV. THE STARTING MODEL WAS A 2.4 ANGSTROM STRUCTURE WITH A DIFFERENT ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THESE ARE RE-REFINED COORDINATES OF THE PREVIOUS WWPDB SUBMISSION 1TXV. THE STARTING MODEL WAS A 2.4 ANGSTROM STRUCTURE WITH A DIFFERENT BOUND LIGAND. THE MODEL IS REFINED TO LOWER RFREE. ONE SEQUENCE MISTAKE IN THE AIIB SUBUNIT IS CORRECTED. MORE OF BETA SUBUNIT DOMAIN I-EGF1 IS BUILT. MISTAKES IN CARBOHYDRATE ANOMERIC LINKAGES ARE CORRECTED.
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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: 36.91 Å2
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Refinement step | Cycle: LAST / Resolution: 2.75→42.99 Å
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Refine LS restraints |
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