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Open data
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Basic information
Entry | Database: PDB / ID: 5h9v | ||||||
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Title | Crystal structure of Regnase PIN domain, form I | ||||||
![]() | Ribonuclease ZC3H12A | ||||||
![]() | HYDROLASE / RNase | ||||||
Function / homology | ![]() immune response-activating signaling pathway / positive regulation of miRNA catabolic process / positive regulation of protein deubiquitination / cellular response to ionomycin / miRNA catabolic process / RNA exonuclease activity / positive regulation of mRNA catabolic process / rough endoplasmic reticulum membrane / negative regulation by host of viral genome replication / cellular response to sodium arsenite ...immune response-activating signaling pathway / positive regulation of miRNA catabolic process / positive regulation of protein deubiquitination / cellular response to ionomycin / miRNA catabolic process / RNA exonuclease activity / positive regulation of mRNA catabolic process / rough endoplasmic reticulum membrane / negative regulation by host of viral genome replication / cellular response to sodium arsenite / negative regulation of T-helper 17 cell differentiation / negative regulation of muscle cell apoptotic process / nuclease activity / 3'-UTR-mediated mRNA destabilization / positive regulation of lipid storage / negative regulation of cardiac muscle contraction / negative regulation of nitric oxide biosynthetic process / mRNA 3'-UTR AU-rich region binding / cellular response to chemokine / negative regulation of non-canonical NF-kappaB signal transduction / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / miRNA binding / negative regulation of interleukin-1 beta production / positive regulation of p38MAPK cascade / negative regulation of NF-kappaB transcription factor activity / protein deubiquitination / positive regulation of execution phase of apoptosis / mRNA catabolic process / negative regulation of interleukin-6 production / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / negative regulation of cytokine production involved in inflammatory response / positive regulation of fat cell differentiation / cellular response to interleukin-1 / cellular response to glucose starvation / positive regulation of autophagy / negative regulation of canonical NF-kappaB signal transduction / rough endoplasmic reticulum / positive regulation of defense response to virus by host / RNA endonuclease activity / positive regulation of endothelial cell migration / negative regulation of protein phosphorylation / mRNA 3'-UTR binding / P-body / cellular response to virus / cytoplasmic ribonucleoprotein granule / positive regulation of protein import into nucleus / RNA stem-loop binding / positive regulation of angiogenesis / positive regulation of reactive oxygen species metabolic process / ribosome binding / protein complex oligomerization / cellular response to tumor necrosis factor / nervous system development / T cell receptor signaling pathway / cellular response to oxidative stress / cellular response to lipopolysaccharide / angiogenesis / cysteine-type deubiquitinase activity / Hydrolases; Acting on ester bonds / cell differentiation / cytoskeleton / inflammatory response / negative regulation of gene expression / mRNA binding / apoptotic process / DNA damage response / chromatin binding / positive regulation of gene expression / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yokogawa, M. / Tsushima, T. / Adachi, W. / Noda, N.N. / Inagaki, F. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for the regulation of enzymatic activity of Regnase-1 by domain-domain interactions Authors: Yokogawa, M. / Tsushima, T. / Noda, N.N. / Kumeta, H. / Enokizono, Y. / Yamashita, K. / Standley, D.M. / Takeuchi, O. / Akira, S. / Inagaki, F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 280.3 KB | Display | ![]() |
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PDB format | ![]() | 238.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 460 KB | Display | ![]() |
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Full document | ![]() | 470.4 KB | Display | |
Data in XML | ![]() | 23.9 KB | Display | |
Data in CIF | ![]() | 32.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper:
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Components
#1: Protein | Mass: 24717.869 Da / Num. of mol.: 4 / Fragment: PIN domain, UNP residues 134-339 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q5D1E7, Hydrolases; Acting on ester bonds #2: Chemical | ChemComp-NA / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.52 Å3/Da / Density % sol: 65.03 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 1 M (NH4)2HPO4, 200 mM NaCl, 100 mM sodium citrate |
-Data collection
Diffraction | Mean temperature: 95 K | ||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 8, 2009 | ||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.75→47.49 Å / Num. obs: 33467 / % possible obs: 90.5 % / Redundancy: 7.9 % / Net I/σ(I): 22.2 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 92.716 Å2
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Refinement step | Cycle: 1 / Resolution: 2.75→47.49 Å
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Refine LS restraints |
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