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Yorodumi- PDB-4ylq: Crystal Structure of a FVIIa-Trypsin Chimera (FT) in Complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ylq | |||||||||
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Title | Crystal Structure of a FVIIa-Trypsin Chimera (FT) in Complex with Soluble Tissue Factor | |||||||||
Components |
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Keywords | HYDROLASE / trypsin-fold / protein-protein complex | |||||||||
Function / homology | Function and homology information activation of blood coagulation via clotting cascade / activation of plasma proteins involved in acute inflammatory response / coagulation factor VIIa / response to Thyroid stimulating hormone / response to 2,3,7,8-tetrachlorodibenzodioxine / response to astaxanthin / response to thyrotropin-releasing hormone / response to genistein / serine-type peptidase complex / positive regulation of platelet-derived growth factor receptor signaling pathway ...activation of blood coagulation via clotting cascade / activation of plasma proteins involved in acute inflammatory response / coagulation factor VIIa / response to Thyroid stimulating hormone / response to 2,3,7,8-tetrachlorodibenzodioxine / response to astaxanthin / response to thyrotropin-releasing hormone / response to genistein / serine-type peptidase complex / positive regulation of platelet-derived growth factor receptor signaling pathway / response to vitamin K / response to carbon dioxide / response to thyroxine / NGF-stimulated transcription / response to cholesterol / response to growth hormone / positive regulation of positive chemotaxis / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of leukocyte chemotaxis / cytokine receptor activity / positive regulation of TOR signaling / positive regulation of blood coagulation / animal organ regeneration / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Removal of aminoterminal propeptides from gamma-carboxylated proteins / positive regulation of endothelial cell proliferation / serine-type peptidase activity / BMAL1:CLOCK,NPAS2 activates circadian gene expression / positive regulation of interleukin-8 production / protein processing / phospholipid binding / cytokine-mediated signaling pathway / Golgi lumen / circadian rhythm / response to estrogen / positive regulation of angiogenesis / activation of cysteine-type endopeptidase activity involved in apoptotic process / blood coagulation / response to estradiol / collagen-containing extracellular matrix / protease binding / vesicle / response to hypoxia / positive regulation of cell migration / endoplasmic reticulum lumen / external side of plasma membrane / serine-type endopeptidase activity / signaling receptor binding / calcium ion binding / positive regulation of gene expression / cell surface / extracellular space / extracellular region / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å | |||||||||
Model details | A human-FVIIa Variant with the 170-loop swapped with that from human-Trypsin, and an additional ...A human-FVIIa Variant with the 170-loop swapped with that from human-Trypsin, and an additional replacement of Tyr170b with Phe | |||||||||
Authors | Sorensen, A.B. / Svensson, L.A. / Gandhi, P.S. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2016 Title: Molecular Basis of Enhanced Activity in Factor VIIa-Trypsin Variants Conveys Insights into Tissue Factor-mediated Allosteric Regulation of Factor VIIa Activity. Authors: Sorensen, A.B. / Madsen, J.J. / Svensson, L.A. / Pedersen, A.A. / stergaard, H. / Overgaard, M.T. / Olsen, O.H. / Gandhi, P.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ylq.cif.gz | 386.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ylq.ent.gz | 317 KB | Display | PDB format |
PDBx/mmJSON format | 4ylq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ylq_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4ylq_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4ylq_validation.xml.gz | 33.1 KB | Display | |
Data in CIF | 4ylq_validation.cif.gz | 48.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yl/4ylq ftp://data.pdbj.org/pub/pdb/validation_reports/yl/4ylq | HTTPS FTP |
-Related structure data
Related structure data | 4z6aC 4zmaC 1danS C: citing same article (ref.) 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
-Coagulation factor ... , 2 types, 2 molecules LH
#1: Protein | Mass: 17487.076 Da / Num. of mol.: 1 Fragment: BLOOD COAGULATION FACTOR VIIA LIGHT CHAIN, UNP residues 61-212 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue: Blood / Gene: F7 / Organ: Kidney / Plasmid: pQMCF-5 Details (production host): Cells were licensed from Icosagen (Estonia) Cell line (production host): CHOEBNALT85 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P08709, coagulation factor VIIa |
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#2: Protein | Mass: 27508.611 Da / Num. of mol.: 1 / Fragment: UNP residues 213-466 / Mutation: [169-175] LQQSRKVGDSPN - EASFPGK Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue: Blood / Gene: F7 / Organ: Kidney / Plasmid: pQMCF-5 Details (production host): Cells were licensed from Icosagen (Estonia) Cell line (production host): CHOEBNALT85 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P08709, coagulation factor VIIa |
-Protein , 1 types, 1 molecules T
#3: Protein | Mass: 24826.512 Da / Num. of mol.: 1 / Fragment: UNP residues 33-251 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue: Blood / Gene: F3 / Plasmid: pET3a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Origami 2 / References: UniProt: P13726 |
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-Sugars , 2 types, 2 molecules
#4: Polysaccharide | alpha-D-xylopyranose-(1-3)-alpha-D-xylopyranose-(1-3)-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#6: Sugar | ChemComp-FUC / |
-Non-polymers , 5 types, 608 molecules
#5: Chemical | ChemComp-CA / #7: Chemical | ChemComp-TMA / #8: Chemical | ChemComp-0Z7 / | Mass: 546.081 Da / Num. of mol.: 1 / Fragment: UNP residues 213-466 / Mutation: [169-175] LQQSRKVGDSPN - EASFPGK Source method: isolated from a genetically manipulated source Formula: C27H38ClN6O4 / Source: (gene. exp.) Homo sapiens (human) / Tissue: Blood / Gene: F7 / Organ: Kidney / Plasmid: pQMCF-5 Details (production host): Cells were licensed from Icosagen (Estonia) Cell line (production host): CHOEBNALT85 / Production host: Cricetulus griseus (Chinese hamster) / References: coagulation factor VIIa #9: Chemical | ChemComp-POL / | #10: 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: 2.52 Å3/Da / Density % sol: 51.23 % / Description: Elongated hexgonal prisms |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.1M NaCitrate, 16.6% PEG 3350, 12.5% 1-Propanol, with seeding |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 18, 2014 Details: Rh-coated Si mirrors: M1 collimating mirror, M2 toroidal focusing mirror | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.4→33.57 Å / Num. all: 138932 / Num. obs: 138932 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 15.27 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.094 / Rrim(I) all: 0.101 / Χ2: 1.007 / Net I/σ(I): 14.07 / Num. measured all: 1011012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: In-House FVIIa-WT:sTF-FFR similar to 1DAN Resolution: 1.4→34.253 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.31 / 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: 84.64 Å2 / Biso mean: 26.4558 Å2 / Biso min: 7.7 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.4→34.253 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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