+Open data
-Basic information
Entry | Database: PDB / ID: 5cuf | |||||||||
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Title | X-ray crystal structure of SeMet human Sestrin2 | |||||||||
Components | Sestrin-2SESN2 | |||||||||
Keywords | OXIDOREDUCTASE / alkylhydroperoxidase | |||||||||
Function / homology | Function and homology information regulation of response to reactive oxygen species / negative regulation of translation in response to endoplasmic reticulum stress / sulfiredoxin activity / L-leucine binding / Atg1/ULK1 kinase complex / cellular response to leucine starvation / PH domain binding / oxidoreductase activity, acting on peroxide as acceptor / TORC2 complex / regulation of TORC1 signaling ...regulation of response to reactive oxygen species / negative regulation of translation in response to endoplasmic reticulum stress / sulfiredoxin activity / L-leucine binding / Atg1/ULK1 kinase complex / cellular response to leucine starvation / PH domain binding / oxidoreductase activity, acting on peroxide as acceptor / TORC2 complex / regulation of TORC1 signaling / mitochondrial DNA metabolic process / cellular response to L-leucine / Amino acids regulate mTORC1 / triglyceride homeostasis / nucleotide-activated protein kinase complex / GDP-dissociation inhibitor activity / positive regulation of lipophagy / cellular oxidant detoxification / regulation of gluconeogenesis / fatty acid beta-oxidation / glucose import / positive regulation of macroautophagy / DNA damage response, signal transduction by p53 class mediator / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / cellular response to glucose starvation / response to glucose / negative regulation of TORC1 signaling / positive regulation of TORC1 signaling / cellular response to amino acid starvation / reactive oxygen species metabolic process / protein sequestering activity / phosphatidylinositol 3-kinase/protein kinase B signal transduction / cellular response to amino acid stimulus / TP53 Regulates Metabolic Genes / peroxidase activity / regulation of protein phosphorylation / response to insulin / negative regulation of cell growth / positive regulation of protein localization to nucleus / KEAP1-NFE2L2 pathway / glucose homeostasis / cellular response to oxidative stress / lysosomal membrane / protein-containing complex binding / mitochondrion / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.5 Å | |||||||||
Authors | Kim, H. / An, S. / Ro, S.-H. / Lee, J.H. / Cho, U.-S. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nat Commun / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5cuf.cif.gz | 377.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5cuf.ent.gz | 320.5 KB | Display | PDB format |
PDBx/mmJSON format | 5cuf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cu/5cuf ftp://data.pdbj.org/pub/pdb/validation_reports/cu/5cuf | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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5 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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.) Homo sapiens (human) / Gene: SESN2, SEST2 / Production host: Escherichia coli (E. coli) / References: UniProt: P58004 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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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: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97879 Å | |||||||||
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 |
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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 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 3.5→44.12 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.885 / SU B: 23.627 / SU ML: 0.358 / Cross valid method: THROUGHOUT / ESU R Free: 0.532 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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