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Yorodumi- PDB-6gwq: Crystal Structure of Stabilized Active Plasminogen Activator Inhi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6gwq | |||||||||
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Title | Crystal Structure of Stabilized Active Plasminogen Activator Inhibitor-1 (PAI-1-stab) in Complex with an Inhibitory Nanobody (VHH-2g-42) | |||||||||
Components |
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Keywords | HYDROLASE / plasminogen activator inhibitor-1 / PAI-1 / PAI-1-stab / serpin / protease inhibitor / serine protease inhibitor / nanobody / antibody fragment / protein complex | |||||||||
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 receptor-mediated endocytosis / positive regulation of inflammatory response / positive regulation of angiogenesis / Platelet degranulation / cellular response to lipopolysaccharide / angiogenesis / defense response to Gram-negative bacterium / collagen-containing extracellular matrix / protease binding / signaling receptor binding / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Vicugna pacos (alpaca) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.32 Å | |||||||||
Authors | Sillen, M. / Weeks, S.D. / Strelkov, S.V. / Declerck, P.J. | |||||||||
Funding support | Belgium, 2items
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Citation | Journal: J.Thromb.Haemost. / Year: 2020 Title: Molecular mechanism of two nanobodies that inhibit PAI-1 activity reveals a modulation at distinct stages of the PAI-1/plasminogen activator interaction. Authors: Sillen, M. / Weeks, S.D. / Zhou, X. / Komissarov, A.A. / Florova, G. / Idell, S. / Strelkov, S.V. / Declerck, P.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6gwq.cif.gz | 194.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gwq.ent.gz | 153.5 KB | Display | PDB format |
PDBx/mmJSON format | 6gwq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6gwq_validation.pdf.gz | 426 KB | Display | wwPDB validaton report |
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Full document | 6gwq_full_validation.pdf.gz | 430.5 KB | Display | |
Data in XML | 6gwq_validation.xml.gz | 17.5 KB | Display | |
Data in CIF | 6gwq_validation.cif.gz | 23.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gw/6gwq ftp://data.pdbj.org/pub/pdb/validation_reports/gw/6gwq | HTTPS FTP |
-Related structure data
Related structure data | 6gwnC 6gwpC 1db2S 5ja8S S: Starting model for refinement C: citing same article (ref.) |
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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: 42751.008 Da / Num. of mol.: 1 / Mutation: N150H-K154T-Q301P-Q319L-M354I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINE1 / Plasmid: pETHSUK2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 pLysS / References: UniProt: P05121 |
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#2: Antibody | Mass: 12752.254 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vicugna pacos (alpaca) / Plasmid: pETHSUK2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 pLysS |
#3: 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: 2.49 Å3/Da / Density % sol: 50.67 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1 M succinic acid, 0.1 M HEPES, 1 % w/v PEG 2000 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980105 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 12, 2017 Details: convex prefocussing mirror and a Kirkpatrick-Baez pair of focussing mirrors | ||||||||||||||||||||||||||||||
Radiation | Monochromator: Cryogenically cooled channel cut crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.980105 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.14→60.19 Å / Num. obs: 29859 / % possible obs: 99.7 % / Redundancy: 3.9 % / Biso Wilson estimate: 49.45 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.05 / Rrim(I) all: 0.099 / Net I/σ(I): 8.2 / Num. measured all: 115386 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DB2, 5JA8 Resolution: 2.32→49.816 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0.33 / Phase error: 24.81 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 121.31 Å2 / Biso mean: 55.0693 Å2 / Biso min: 27.46 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.32→49.816 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8
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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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