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- PDB-1rf1: Crystal Structure of Fragment D of gammaE132A Fibrinogen with the... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1rf1 | |||||||||
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Title | Crystal Structure of Fragment D of gammaE132A Fibrinogen with the Peptide Ligand Gly-His-Arg-Pro-amide | |||||||||
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![]() | BLOOD CLOTTING / BLOOD COAGULATION / FIBRINOGEN / FIBRINOGEN FRAGMENT D / RECOMBINANT FIBRINOGEN FRAGMENT D / fragment D of gammaE132A / FIBRINOGEN with GHRP-amide | |||||||||
Function / homology | ![]() 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 / protein secretion / protein polymerization / cellular response to interleukin-1 / 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 / positive regulation of vasoconstriction / 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 / MAP2K and MAPK activation / platelet aggregation / response to calcium ion / 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 / cell cortex / ER-Phagosome pathway / protein-folding chaperone binding / 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 | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Kostelansky, M.S. / Gorkun, O.V. / Lord, S.T. | |||||||||
![]() | ![]() Title: Calcium-Binding Site beta2, Adjacent to the "b" Polymerization Site, Modulates Lateral Aggregation of Protofibrils during Fibrin Polymerization. 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 280.9 KB | Display | ![]() |
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PDB format | ![]() | 225.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 54.2 KB | Display | |
Data in CIF | ![]() | 74.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1rf0C ![]() 1ltjS S: Starting model for refinement 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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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: Fibrinogen alpha/alpha-E Chain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 35940.215 Da / Num. of mol.: 2 / Fragment: Fibrinogen Bbeta Chain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | Mass: 35159.957 Da / Num. of mol.: 2 / Fragment: Fibrinogen gamma chain / Mutation: E132A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Protein/peptide / Sugars , 2 types, 6 molecules GHIJ
#4: Protein/peptide | Mass: 467.522 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: The peptide was chemically synthesized. #5: Polysaccharide | Source method: isolated from a genetically manipulated source |
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-Non-polymers , 2 types, 252 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | ChemComp-CA / #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.49 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 9-10% PEG 3350, 12.5 mM calcium chloride, 2 mM sodium azide, 50 mM Tris pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.4 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 12, 2003 Details: Flat mirror (vertical focusing); single crystal Si(311) bent monochromator (horizontal focusing) |
Radiation | Monochromator: Flat mirror (vertical focusing); single crystal Si(311) bent monochromator (horizontal focusing) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98396 Å / Relative weight: 1 |
Reflection | Resolution: 2.53→18 Å / Num. obs: 66025 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 33.8 Å2 / Rsym value: 0.09 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 2.53→2.62 Å / Mean I/σ(I) obs: 4 / Num. unique all: 6506 / Rsym value: 0.359 / % possible all: 100 |
Reflection | *PLUS Lowest resolution: 18 Å / Num. measured all: 264892 / Rmerge(I) obs: 0.09 |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.359 |
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Processing
Software |
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Refinement | Method to determine structure: rigid body refinement Starting model: pdb entry 1LTJ Resolution: 2.53→17.97 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2084524.44 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 34.1769 Å2 / ksol: 0.333272 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.53→17.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.53→2.69 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 18 Å / % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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