+Open data
-Basic information
Entry | Database: PDB / ID: 3r4l | |||||||||
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Title | Human very long half life Plasminogen Activator Inhibitor type-1 | |||||||||
Components | Plasminogen activator inhibitor 1 | |||||||||
Keywords | BLOOD CLOTTING / serine protease inhibitor / PAI-1 / very long half life / plasminogen activator inhibitor type 1 / carbohydrate | |||||||||
Function / homology | Function and homology information positive regulation of leukotriene production involved in inflammatory response / dentinogenesis / negative regulation of smooth muscle cell-matrix adhesion / negative regulation of smooth muscle cell migration / peptidase inhibitor complex / negative regulation of vascular wound healing / negative regulation of wound healing / positive regulation of odontoblast differentiation / negative regulation of cell adhesion mediated by integrin / negative regulation of endopeptidase activity ...positive regulation of leukotriene production involved in inflammatory response / dentinogenesis / negative regulation of smooth muscle cell-matrix adhesion / negative regulation of smooth muscle cell migration / peptidase inhibitor complex / negative regulation of vascular wound healing / negative regulation of wound healing / positive regulation of odontoblast differentiation / negative regulation of cell adhesion mediated by integrin / negative regulation of endopeptidase activity / negative regulation of plasminogen activation / negative regulation of blood coagulation / regulation of signaling receptor activity / positive regulation of monocyte chemotaxis / Dissolution of Fibrin Clot / replicative senescence / ECM proteoglycans / positive regulation of blood coagulation / negative regulation of fibrinolysis / negative regulation of endothelial cell apoptotic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / serine protease inhibitor complex / fibrinolysis / negative regulation of cell migration / BMAL1:CLOCK,NPAS2 activates circadian gene expression / platelet alpha granule lumen / positive regulation of interleukin-8 production / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / serine-type endopeptidase inhibitor activity / positive regulation of inflammatory response / positive regulation of receptor-mediated endocytosis / positive regulation of angiogenesis / Platelet degranulation / angiogenesis / collagen-containing extracellular matrix / cellular response to lipopolysaccharide / protease binding / defense response to Gram-negative bacterium / signaling receptor binding / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | |||||||||
Authors | Yang, J. / Zheng, H. / Han, Q. / Skrzypczak-Jankun, E. / Jankun, J. | |||||||||
Citation | Journal: Int.J.Mol.Med. / Year: 2012 Title: Remarkable extension of PAI-1 half-life surprisingly brings no changes to its structure. Authors: Jankun, J. / Yang, J. / Zheng, H. / Han, F.Q. / Al-Senaidy, A. / Skrzypczak-Jankun, E. #1: Journal: Mol.Cancer Ther. / Year: 2003 Title: A novel form of the plasminogen activator inhibitor created by cysteine mutations extends its half-life: relevance to cancer and angiogenesis. Authors: Chorostowska-Wynimko, J. / Swiercz, R. / Skrzypczak-Jankun, E. / Wojtowicz, A. / Selman, S.H. / Jankun, J. #2: Journal: Int.J.Mol.Med. / Year: 2009 Title: VLHL plasminogen activator inhibitor spontaneously reactivates from the latent to active form. Authors: Jankun, J. / Aleem, A.M. / Selman, S.H. / Basrur, V. / Skrzypczak-Jankun, E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3r4l.cif.gz | 93.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3r4l.ent.gz | 69.1 KB | Display | PDB format |
PDBx/mmJSON format | 3r4l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r4/3r4l ftp://data.pdbj.org/pub/pdb/validation_reports/r4/3r4l | HTTPS FTP |
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-Related structure data
Related structure data | 9paiS S: Starting model for refinement |
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Similar 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: 42840.172 Da / Num. of mol.: 1 / Fragment: UNP Residues 24-402 / Mutation: Q197C, G355C Source method: isolated from a genetically manipulated source Details: Active form / Source: (gene. exp.) Homo sapiens (human) / Gene: PAI1, PLANH1, SERPINE1 / Plasmid: PFASTBAC1 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P05121 |
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#2: Polysaccharide | beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4) ...beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Sugar | ChemComp-NAG / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.4 Å3/Da / Density % sol: 64 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.025M NACL, 27% TERT-BUTANOL, 0.050M TRIS-HCL, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 1, 2010 |
Radiation | Monochromator: Asymmetric curved crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.699→33.003 Å / Num. obs: 13852 / % possible obs: 82.4 % / Observed criterion σ(I): 1 / Redundancy: 4 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 2.699→2.8 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 2.5 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 9PAI Resolution: 2.7→33 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.925 / SU B: 15.309 / SU ML: 0.31 / Cross valid method: THROUGHOUT / ESU R: 1.367 / ESU R Free: 0.408 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 68.8 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.77 Å / Total num. of bins used: 20
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