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Open data
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Basic information
Entry | Database: PDB / ID: 5cuf | |||||||||
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Title | X-ray crystal structure of SeMet human Sestrin2 | |||||||||
![]() | Sestrin-2 | |||||||||
![]() | OXIDOREDUCTASE / alkylhydroperoxidase | |||||||||
Function / homology | ![]() regulation of response to reactive oxygen species / sulfiredoxin activity / negative regulation of translation in response to endoplasmic reticulum stress / L-leucine binding / Atg1/ULK1 kinase complex / TORC2 complex / regulation of TORC1 signaling / oxidoreductase activity, acting on peroxide as acceptor / cellular response to leucine starvation / PH domain binding ...regulation of response to reactive oxygen species / sulfiredoxin activity / negative regulation of translation in response to endoplasmic reticulum stress / L-leucine binding / Atg1/ULK1 kinase complex / TORC2 complex / regulation of TORC1 signaling / oxidoreductase activity, acting on peroxide as acceptor / cellular response to leucine starvation / PH domain binding / mitochondrial DNA metabolic process / nucleotide-activated protein kinase complex / regulation of cAMP/PKA signal transduction / Amino acids regulate mTORC1 / cellular response to L-leucine / positive regulation of lipophagy / GDP-dissociation inhibitor activity / triglyceride homeostasis / regulation of gluconeogenesis / cellular oxidant detoxification / fatty acid beta-oxidation / D-glucose import / regulation of protein phosphorylation / positive regulation of macroautophagy / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / response to glucose / cellular response to glucose starvation / negative regulation of TORC1 signaling / positive regulation of TORC1 signaling / reactive oxygen species metabolic process / protein sequestering activity / cellular response to amino acid starvation / TP53 Regulates Metabolic Genes / cellular response to amino acid stimulus / DNA damage response, signal transduction by p53 class mediator / peroxidase activity / negative regulation of cell growth / response to insulin / positive regulation of protein localization to nucleus / KEAP1-NFE2L2 pathway / glucose homeostasis / cellular response to oxidative stress / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / lysosomal membrane / protein-containing complex binding / mitochondrion / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Kim, H. / An, S. / Ro, S.-H. / Lee, J.H. / Cho, U.-S. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Janus-faced Sestrin2 controls ROS and mTOR signalling through two separate functional domains. Authors: Kim, H. / An, S. / Ro, S.H. / Teixeira, F. / Jin Park, G. / Kim, C. / Cho, C.S. / Kim, J.S. / Jakob, U. / Hee Lee, J. / Cho, U.S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 382.3 KB | Display | ![]() |
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PDB format | ![]() | 313.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 476.1 KB | Display | ![]() |
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Full document | ![]() | 508.5 KB | Display | |
Data in XML | ![]() | 63.4 KB | Display | |
Data in CIF | ![]() | 86.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: _ / Auth seq-ID: 66 - 478 / Label seq-ID: 69 - 481
NCS ensembles :
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Components
#1: Protein | Mass: 55442.457 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Has protein modification | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.79 Å3/Da / Density % sol: 67.52 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M MES 1.15 M sodium malonate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 6, 2014 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97879 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→44.12 Å / Num. obs: 52390 / % possible obs: 99.9 % / Redundancy: 88.6 % / Rmerge(I) obs: 0.305 / Net I/σ(I): 28.5 |
Reflection shell | Resolution: 3.5→3.59 Å / Redundancy: 3.7 % / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 103.032 Å2
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Refinement step | Cycle: LAST / Resolution: 3.5→44.12 Å
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Refine LS restraints |
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