+Open data
-Basic information
Entry | Database: PDB / ID: 5m3y | |||||||||
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Title | Crystal structure of human glycosylated angiotensinogen | |||||||||
Components | AngiotensinogenAngiotensin | |||||||||
Keywords | Serine protease inhibitor / glycosylated / human angiotensiogen | |||||||||
Function / homology | Function and homology information regulation of blood volume by renin-angiotensin / response to muscle activity involved in regulation of muscle adaptation / regulation of renal sodium excretion / : / type 2 angiotensin receptor binding / maintenance of blood vessel diameter homeostasis by renin-angiotensin / negative regulation of neurotrophin TRK receptor signaling pathway / regulation of extracellular matrix assembly / positive regulation of activation of Janus kinase activity / regulation of renal output by angiotensin ...regulation of blood volume by renin-angiotensin / response to muscle activity involved in regulation of muscle adaptation / regulation of renal sodium excretion / : / type 2 angiotensin receptor binding / maintenance of blood vessel diameter homeostasis by renin-angiotensin / negative regulation of neurotrophin TRK receptor signaling pathway / regulation of extracellular matrix assembly / positive regulation of activation of Janus kinase activity / regulation of renal output by angiotensin / positive regulation of NAD(P)H oxidase activity / G protein-coupled receptor signaling pathway coupled to cGMP nucleotide second messenger / renin-angiotensin regulation of aldosterone production / renal system process / positive regulation of branching involved in ureteric bud morphogenesis / positive regulation of CoA-transferase activity / positive regulation of extracellular matrix assembly / positive regulation of macrophage derived foam cell differentiation / low-density lipoprotein particle remodeling / vasoconstriction / type 1 angiotensin receptor binding / response to angiotensin / positive regulation of extrinsic apoptotic signaling pathway / positive regulation of epidermal growth factor receptor signaling pathway / positive regulation of cardiac muscle hypertrophy / positive regulation of gap junction assembly / regulation of vasoconstriction / regulation of cardiac conduction / positive regulation of epithelial to mesenchymal transition / blood vessel remodeling / positive regulation of protein tyrosine kinase activity / Metabolism of Angiotensinogen to Angiotensins / nitric oxide mediated signal transduction / positive regulation of protein metabolic process / Peptide ligand-binding receptors / negative regulation of MAP kinase activity / positive regulation of endothelial cell migration / kidney development / regulation of cell growth / positive regulation of cytokine production / angiotensin-activated signaling pathway / growth factor activity / serine-type endopeptidase inhibitor activity / hormone activity / PPARA activates gene expression / regulation of blood pressure / positive regulation of inflammatory response / positive regulation of miRNA transcription / positive regulation of reactive oxygen species metabolic process / positive regulation of fibroblast proliferation / cell-cell signaling / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of NF-kappaB transcription factor activity / regulation of cell population proliferation / G alpha (i) signalling events / G alpha (q) signalling events / collagen-containing extracellular matrix / blood microparticle / regulation of apoptotic process / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / G protein-coupled receptor signaling pathway / positive regulation of DNA-templated transcription / extracellular space / extracellular exosome / extracellular region / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Yan, Y. / Read, R.J. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: J. Biol. Chem. / Year: 2019 Title: Structural basis for the specificity of renin-mediated angiotensinogen cleavage. Authors: Yan, Y. / Zhou, A. / Carrell, R.W. / Read, R.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5m3y.cif.gz | 252.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5m3y.ent.gz | 208.8 KB | Display | PDB format |
PDBx/mmJSON format | 5m3y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m3/5m3y ftp://data.pdbj.org/pub/pdb/validation_reports/m3/5m3y | HTTPS FTP |
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-Related structure data
Related structure data | 5m3xC 6i3fC 6i3iC 2wxwS 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: 50647.656 Da / Num. of mol.: 1 / Mutation: N137Q, N271Q, N295Q, C232S, C308S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AGT, SERPINA8 / Plasmid: pCEP4 / Cell (production host): HEK293 EBNA / Production host: Homo sapiens (human) / References: UniProt: P01019 |
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#2: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#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: 3.15 Å3/Da / Density % sol: 60.94 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 2.0M Ammonium Sulfate, 0.1M Bicine, pH9.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.987 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 6, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→46.8 Å / Num. obs: 27827 / % possible obs: 99.9 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.702 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2WXW Resolution: 2.3→46.8 Å / Cross valid method: NONE / σ(F): 1.36 / Phase error: 28.8
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→46.8 Å
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Refine LS restraints |
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LS refinement shell |
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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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