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Yorodumi- PDB-3fib: RECOMBINANT HUMAN GAMMA-FIBRINOGEN CARBOXYL TERMINAL FRAGMENT (RE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fib | ||||||
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Title | RECOMBINANT HUMAN GAMMA-FIBRINOGEN CARBOXYL TERMINAL FRAGMENT (RESIDUES 143-411) BOUND TO CALCIUM AT PH 6.0: A FURTHER REFINEMENT OF PDB ENTRY 1FIB, AND DIFFERS FROM 1FIB BY THE MODELLING OF A CIS PEPTIDE BOND BETWEEN RESIDUES K338 AND C339 | ||||||
Components | FIBRINOGEN GAMMA CHAIN RESIDUES | ||||||
Keywords | BLOOD COAGULATION / FIBRINOGEN / FIBRIN POLYMERIZATION / CIS PEPTIDE BONDS | ||||||
Function / homology | Function and homology information platelet maturation / fibrinogen complex / Regulation of TLR by endogenous ligand / blood coagulation, fibrin clot formation / platelet alpha granule / 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 / blood coagulation, fibrin clot formation / platelet alpha granule / 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 / positive regulation of substrate adhesion-dependent cell spreading / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of vasoconstriction / fibrinolysis / cell adhesion molecule binding / cell-matrix adhesion / Integrin signaling / platelet alpha granule lumen / Post-translational protein phosphorylation / positive regulation of protein secretion / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / platelet aggregation / response to calcium ion / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / 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 / Signaling by BRAF and RAF1 fusions / Platelet degranulation / ER-Phagosome pathway / collagen-containing extracellular matrix / protein-containing complex assembly / blood microparticle / positive regulation of ERK1 and ERK2 cascade / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 2.1 Å | ||||||
Authors | Pratt, K.P. / Cote, H.C.F. / Chung, D.W. / Stenkamp, R.E. / Davie, E.W. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1997 Title: The primary fibrin polymerization pocket: three-dimensional structure of a 30-kDa C-terminal gamma chain fragment complexed with the peptide Gly-Pro-Arg-Pro. Authors: Pratt, K.P. / Cote, H.C. / Chung, D.W. / Stenkamp, R.E. / Davie, E.W. #1: Journal: Structure / Year: 1997 Title: Crystal Structure of a 30 kDa C-Terminal Fragment from the Gamma Chain of Human Fibrinogen Authors: Yee, V.C. / Pratt, K.P. / Cote, H.Cf. / Le Trong, I. / Chung, D.W. / Davie, E.W. / Stenkamp, R.E. / Teller, D.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fib.cif.gz | 62.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fib.ent.gz | 48.1 KB | Display | PDB format |
PDBx/mmJSON format | 3fib.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fi/3fib ftp://data.pdbj.org/pub/pdb/validation_reports/fi/3fib | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28256.275 Da / Num. of mol.: 1 / Fragment: RESIDUES 143 - 411 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Organ: BLOOD / Plasmid: PPIC9K / Production host: Pichia pastoris (fungus) / Strain (production host): GS115 / References: UniProt: P02679 |
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#2: Chemical | ChemComp-CA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 35 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6 Details: 18% PEG 8000, 0.1 M MES PH 6.0, 70MM CACL2, SITTING DROP VAPOR DIFFUSION | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 300 K |
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Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Aug 1, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.03→33 Å / Num. obs: 12334 / % possible obs: 82.7 % / Observed criterion σ(I): 1 / Redundancy: 1.5 % / Rmerge(I) obs: 0.0333 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.1→10 Å Details: THERE WAS NO APPARENT ELECTRON DENSITY FOR C-TERMINAL RESIDUES 393 - 411. PROTEOLYSIS AT THE C-TERMINUS WAS CONFIRMED BY MASS SPECTROMETRY.
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Refinement step | Cycle: LAST / Resolution: 2.1→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→10 Å / Rfactor Rfree: 0.2318 / Rfactor Rwork: 0.1702 / Total num. of bins used: 20 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor obs: 0.1702 |