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Yorodumi- PDB-2oyi: Crystal Structure of Fragment D of gammaD298,301A Fibrinogen with... -
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-Basic information
Entry | Database: PDB / ID: 2oyi | |||||||||
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Title | Crystal Structure of Fragment D of gammaD298,301A Fibrinogen with the Peptide Ligand Gly-Pro-Arg-Pro-Amide | |||||||||
Components |
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Keywords | BLOOD CLOTTING / fibrinogen / fibrinogen fragment D / variant fibrinogen / gammaD298 / 301A fibrinogen | |||||||||
Function / homology | Function and homology information platelet maturation / blood coagulation, common pathway / induction of bacterial agglutination / fibrinogen complex / Regulation of TLR by endogenous ligand / platelet alpha granule / blood coagulation, fibrin clot formation / cellular response to leptin stimulus / cellular response to interleukin-6 / MyD88 deficiency (TLR2/4) ...platelet maturation / blood coagulation, common pathway / induction of bacterial agglutination / fibrinogen complex / Regulation of TLR by endogenous ligand / platelet alpha granule / blood coagulation, fibrin clot formation / cellular response to leptin stimulus / 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 / 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 / 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 / extracellular vesicle / Platelet degranulation / protein-macromolecule adaptor activity / protein-folding chaperone binding / ER-Phagosome pathway / cell cortex / protein-containing complex assembly / collagen-containing extracellular matrix / adaptive immune response / positive regulation of ERK1 and ERK2 cascade / blood microparticle / Amyloid fiber formation / endoplasmic reticulum lumen / external side of plasma membrane / innate immune response / signaling receptor binding / synapse / structural molecule activity / cell surface / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / identical protein binding / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | |||||||||
Authors | Kostelansky, M.S. / Gorkun, O.V. / Lord, S.T. | |||||||||
Citation | Journal: Biochemistry / Year: 2007 Title: Probing the gamma2 Calcium-Binding Site: Studies with gammaD298,301A Fibrinogen Reveal Changes in the gamma294-301 Loop that Alter the Integrity of the "a" Polymerization Site. Authors: Kostelansky, M.S. / Lounes, K.C. / Ping, L.F. / Dickerson, S.K. / Gorkun, O.V. / Lord, S.T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2oyi.cif.gz | 271.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2oyi.ent.gz | 225.8 KB | Display | PDB format |
PDBx/mmJSON format | 2oyi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2oyi_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 2oyi_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2oyi_validation.xml.gz | 53.6 KB | Display | |
Data in CIF | 2oyi_validation.cif.gz | 73.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oy/2oyi ftp://data.pdbj.org/pub/pdb/validation_reports/oy/2oyi | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 3 types, 6 molecules ADBECF
#1: Protein | Mass: 7747.030 Da / Num. of mol.: 2 / Fragment: Residues 126-191 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FGA / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): CHO cells / References: UniProt: P02671 #2: Protein | Mass: 35940.215 Da / Num. of mol.: 2 / Fragment: Residues 149-461 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FGB / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): CHO cells / References: UniProt: P02675 #3: Protein | Mass: 35129.973 Da / Num. of mol.: 2 / Fragment: Residues 96-406 / Mutation: D298A, D301A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FGG / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): CHO cells / References: UniProt: P02679 |
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-Protein/peptide / Sugars , 2 types, 6 molecules GHIJ
#4: Protein/peptide | Mass: 426.490 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Chemically synthesized #5: Polysaccharide | Source method: isolated from a genetically manipulated source |
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-Non-polymers , 2 types, 154 molecules
#6: Chemical | ChemComp-CA / #7: 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: 2.97 Å3/Da / Density % sol: 58.6 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 5 microL of 10 mg/mL protein in HBS with 3 mM GPRP were mixed with an identical volume of well solution containing 50 mM Tris, pH 8.5, 2 mM NaN3, 12.5 mM CaCl2, and 11% PEG 3350, VAPOR ...Details: 5 microL of 10 mg/mL protein in HBS with 3 mM GPRP were mixed with an identical volume of well solution containing 50 mM Tris, pH 8.5, 2 mM NaN3, 12.5 mM CaCl2, and 11% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 28, 2003 / Details: Osmic confocal blue multilayer optics |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. all: 52450 / Num. obs: 52450 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 45.3 Å2 / Rsym value: 0.116 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0 / Mean I/σ(I) obs: 3.3 / Num. unique all: 5217 / Rsym value: 0.484 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→17.97 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2035371.67 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 27.1815 Å2 / ksol: 0.330128 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→17.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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