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Yorodumi- PDB-3hus: Crystal structure of recombinant gamma N308K fibrinogen fragment ... -
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-Basic information
Entry | Database: PDB / ID: 3hus | |||||||||
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Title | Crystal structure of recombinant gamma N308K fibrinogen fragment D with the peptide ligand Gly-Pro-Arg-Pro-amide | |||||||||
Components |
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Keywords | BLOOD CLOTTING / Fibrinogen fragment D / Amyloid / Amyloidosis / Blood coagulation / Disease mutation / Disulfide bond / Glycoprotein / Isopeptide bond / Phosphoprotein / Secreted / Pyrrolidone carboxylic acid / Sulfation | |||||||||
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 / 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 | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.04 Å | |||||||||
Authors | Lord, S.T. / Bowley, S.R. / Okumura, N. | |||||||||
Citation | Journal: Biochemistry / Year: 2009 Title: Impaired protofibril formation in fibrinogen gammaN308K is due to altered D:D and "A:a" interactions. Authors: Bowley, S.R. / Okumura, N. / 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 | 3hus.cif.gz | 274.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hus.ent.gz | 220.6 KB | Display | PDB format |
PDBx/mmJSON format | 3hus.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3hus_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3hus_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3hus_validation.xml.gz | 28.9 KB | Display | |
Data in CIF | 3hus_validation.cif.gz | 43.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hu/3hus ftp://data.pdbj.org/pub/pdb/validation_reports/hu/3hus | HTTPS FTP |
-Related structure data
Related structure data | 1ltjS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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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: Fragment D: UNP residues 145-210 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FGA / Plasmid: pMLP / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P02671 #2: Protein | Mass: 35940.215 Da / Num. of mol.: 2 / Fragment: Fragment D: UNP residues 179-491 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FGB / Plasmid: pMLP / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P02675 #3: Protein | Mass: 35233.070 Da / Num. of mol.: 2 / Fragment: Fragment D: UNP residues 122-432 / Mutation: N308K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FGG, PRO2061 / Plasmid: pMLP / Production host: Cricetulus griseus (Chinese hamster) / 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: Peptide Ligand Gly-Pro-Arg-Pro-amide #5: Polysaccharide | Source method: isolated from a genetically manipulated source |
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-Non-polymers , 2 types, 104 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: 3.17 Å3/Da / Density % sol: 61.21 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 9% PEG 3350, 50 mM Tris-HCl pH 8.5, 2 mM Sodium azide, 12.5 mM Calcium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.99 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 22, 2005 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99 Å / Relative weight: 1 |
Reflection | Resolution: 3.04→47.25 Å / Num. obs: 40798 / % possible obs: 99.41 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 61.8 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1LTJ Resolution: 3.04→47.25 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.886 / SU B: 40.077 / SU ML: 0.341 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.487 / 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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 61.947 Å2
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Refinement step | Cycle: LAST / Resolution: 3.04→47.25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.04→3.12 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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