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Yorodumi- PDB-1dug: STRUCTURE OF THE FIBRINOGEN G CHAIN INTEGRIN BINDING AND FACTOR X... -
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-Basic information
Entry | Database: PDB / ID: 1dug | ||||||
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Title | STRUCTURE OF THE FIBRINOGEN G CHAIN INTEGRIN BINDING AND FACTOR XIIIA CROSSLINKING SITES OBTAINED THROUGH CARRIER PROTEIN DRIVEN CRYSTALLIZATION | ||||||
Components | chimera of GLUTATHIONE S-TRANSFERASE-synthetic LINKEr-C-TERMINAL FIBRINOGEN GAMMA CHAIN | ||||||
Keywords | transferase / blood clotting / gamma chain integrin fragment / carrier protein driven crystallization | ||||||
Function / homology | Function and homology information platelet maturation / fibrinogen complex / Regulation of TLR by endogenous ligand / platelet alpha granule / blood coagulation, fibrin clot formation / cellular response to interleukin-6 / MyD88 deficiency (TLR2/4) / positive regulation of heterotypic cell-cell adhesion / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane ...platelet maturation / fibrinogen complex / Regulation of TLR by endogenous ligand / platelet alpha granule / blood coagulation, fibrin clot formation / cellular response to interleukin-6 / MyD88 deficiency (TLR2/4) / positive regulation of heterotypic cell-cell adhesion / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / extracellular matrix structural constituent / plasminogen activation / p130Cas linkage to MAPK signaling for integrins / positive regulation of peptide hormone secretion / positive regulation of exocytosis / GRB2:SOS provides linkage to MAPK signaling for Integrins / positive regulation of vasoconstriction / glutathione transferase / glutathione transferase activity / protein secretion / cellular response to interleukin-1 / protein polymerization / Integrin cell surface interactions / negative regulation of endothelial cell apoptotic process / Common Pathway of Fibrin Clot Formation / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of substrate adhesion-dependent cell spreading / cell adhesion molecule binding / fibrinolysis / glutathione metabolic process / Integrin signaling / cell-matrix adhesion / platelet alpha granule lumen / positive regulation of protein secretion / Post-translational protein phosphorylation / Signaling by high-kinase activity BRAF mutants / response to calcium ion / MAP2K and MAPK activation / platelet aggregation / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Signaling by BRAF and RAF1 fusions / Platelet degranulation / ER-Phagosome pathway / protein-containing complex assembly / collagen-containing extracellular matrix / positive regulation of ERK1 and ERK2 cascade / blood microparticle / endoplasmic reticulum lumen / external side of plasma membrane / signaling receptor binding / structural molecule activity / cell surface / extracellular space / extracellular exosome / extracellular region / identical protein binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Schistosoma japonicum (invertebrata) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å | ||||||
Authors | Ware, S. / Donahue, J.P. / Hawiger, J. / Anderson, W.F. | ||||||
Citation | Journal: Protein Sci. / Year: 1999 Title: Structure of the fibrinogen gamma-chain integrin binding and factor XIIIa cross-linking sites obtained through carrier protein driven crystallization. Authors: Ware, S. / Donahue, J.P. / Hawiger, J. / Anderson, W.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dug.cif.gz | 120.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dug.ent.gz | 94.5 KB | Display | PDB format |
PDBx/mmJSON format | 1dug.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dug_validation.pdf.gz | 758.6 KB | Display | wwPDB validaton report |
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Full document | 1dug_full_validation.pdf.gz | 779 KB | Display | |
Data in XML | 1dug_validation.xml.gz | 29.1 KB | Display | |
Data in CIF | 1dug_validation.cif.gz | 43.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/du/1dug ftp://data.pdbj.org/pub/pdb/validation_reports/du/1dug | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 27133.359 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: GLUTATHIONE S-TRANSFERASE (residues 1-217) bound to synthetic SDP linker (residues 218-220) bound to C-TERMINAL FIBRINOGEN GAMMA CHAIN (residues 221-234) Source: (gene. exp.) Schistosoma japonicum (invertebrata), (gene. exp.) Homo sapiens (human) Description: EUKARYOTA; METAZOA; PLATYHELMINTHES; TREMATODA; DIGENEA; STRIGEIDIDA; SCHISTOSO MATOIDEA; SCHISTOSOMATIDAE; SCHISTOSOMA Gene: FGG,PRO2061 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5ALPHA References: UniProt: P08515, UniProt: P02679, glutathione transferase #2: Chemical | #3: 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: 3.54 Å3/Da / Density % sol: 65.21 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: PEG 3350, sodium acetate, sodium chloride, ammonium sulfate, Tris, reduced glutathione, pH 4.6, VAPOR DIFFUSION, HANGING DROP | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: -170 ℃ | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.0093 |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Mar 15, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0093 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→28 Å / Num. all: 376772 / Num. obs: 67736 / % possible obs: 89.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.56 % / Rmerge(I) obs: 0.054 |
Reflection shell | Resolution: 1.8→2 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.25 / Num. unique all: 12570 / % possible all: 66.1 |
Reflection | *PLUS Num. measured all: 376772 |
Reflection shell | *PLUS % possible obs: 66.1 % |
-Processing
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Refinement | Resolution: 1.8→28 Å / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.8→28 Å
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Refine LS restraints |
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