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- PDB-6i3i: Crystal structure of reactive center loop (RCL) cleaved angiotens... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6i3i | ||||||||||||
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Title | Crystal structure of reactive center loop (RCL) cleaved angiotensinogen | ||||||||||||
![]() | Angiotensinogen | ||||||||||||
![]() | HORMONE / angiotensinogen / reactive center loop | ||||||||||||
Function / homology | ![]() regulation of blood volume by renin-angiotensin / response to muscle activity involved in regulation of muscle adaptation / type 2 angiotensin receptor binding / regulation of renal sodium excretion / maintenance of blood vessel diameter homeostasis by renin-angiotensin / negative regulation of neurotrophin TRK receptor signaling pathway / regulation of extracellular matrix assembly / regulation of renal output by angiotensin / : / G protein-coupled receptor signaling pathway coupled to cGMP nucleotide second messenger ...regulation of blood volume by renin-angiotensin / response to muscle activity involved in regulation of muscle adaptation / type 2 angiotensin receptor binding / regulation of renal sodium excretion / maintenance of blood vessel diameter homeostasis by renin-angiotensin / negative regulation of neurotrophin TRK receptor signaling pathway / regulation of extracellular matrix assembly / regulation of renal output by angiotensin / : / G protein-coupled receptor signaling pathway coupled to cGMP nucleotide second messenger / renal system process / renin-angiotensin regulation of aldosterone production / positive regulation of branching involved in ureteric bud morphogenesis / positive regulation of extracellular matrix assembly / positive regulation of macrophage derived foam cell differentiation / vasoconstriction / positive regulation of CoA-transferase activity / type 1 angiotensin receptor binding / low-density lipoprotein particle remodeling / positive regulation of extrinsic apoptotic signaling pathway / response to angiotensin / positive regulation of epidermal growth factor receptor signaling pathway / positive regulation of cardiac muscle hypertrophy / positive regulation of gap junction assembly / positive regulation of protein tyrosine kinase activity / regulation of vasoconstriction / regulation of cardiac conduction / blood vessel remodeling / Metabolism of Angiotensinogen to Angiotensins / positive regulation of epithelial to mesenchymal transition / nitric oxide-cGMP-mediated signaling / positive regulation of protein metabolic process / positive regulation of endothelial cell migration / Peptide ligand-binding receptors / negative regulation of MAP kinase activity / kidney development / positive regulation of cytokine production / angiotensin-activated signaling pathway / regulation of cell growth / growth factor activity / serine-type endopeptidase inhibitor activity / hormone activity / PPARA activates gene expression / regulation of blood pressure / positive regulation of miRNA transcription / positive regulation of inflammatory response / positive regulation of reactive oxygen species metabolic process / positive regulation of fibroblast proliferation / cell-cell signaling / positive regulation of NF-kappaB transcription factor activity / phospholipase C-activating G protein-coupled receptor signaling pathway / regulation of cell population proliferation / G alpha (i) signalling events / G alpha (q) signalling events / regulation of apoptotic process / collagen-containing extracellular matrix / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / blood microparticle / G protein-coupled receptor signaling pathway / positive regulation of DNA-templated transcription / extracellular space / extracellular exosome / extracellular region / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Yan, Y. / Read, R.J. | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 96.8 KB | Display | ![]() |
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PDB format | ![]() | 72.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 447.5 KB | Display | ![]() |
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Full document | ![]() | 448.5 KB | Display | |
Data in XML | ![]() | 15.8 KB | Display | |
Data in CIF | ![]() | 20.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5m3xC ![]() 5m3yC ![]() 6i3fC ![]() 2wxwS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() |
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#2: Sugar | ChemComp-NAG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.55 Å3/Da / Density % sol: 65.36 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 1.5M ammonium sulfate, 0.1M Tris pH8.5 12% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 23, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.97→66.14 Å / Num. obs: 15316 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.987 / Rmerge(I) obs: 0.214 / Rrim(I) all: 0.254 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 2.97→3.05 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.282 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1106 / CC1/2: 0.53 / Rrim(I) all: 1.505 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2wxw Resolution: 2.97→66.14 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.916 / SU B: 18.186 / SU ML: 0.313 / Cross valid method: THROUGHOUT / ESU R: 1.089 / ESU R Free: 0.343 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 68.732 Å2
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Refinement step | Cycle: 1 / Resolution: 2.97→66.14 Å
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