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- PDB-5t0n: Pseudo-apo structure of Sestrin2 at 3.0 angstrom resolution -

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Basic information

Entry
Database: PDB / ID: 5t0n
TitlePseudo-apo structure of Sestrin2 at 3.0 angstrom resolution
ComponentsSestrin-2
KeywordsSIGNALING PROTEIN / mTOR / signaling / leucine / sestrin
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 / oxidoreductase activity, acting on peroxide as acceptor / TORC2 complex / cellular response to leucine starvation / regulation of TORC1 signaling / PH domain binding ...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 / oxidoreductase activity, acting on peroxide as acceptor / TORC2 complex / cellular response to leucine starvation / regulation of TORC1 signaling / PH domain binding / mitochondrial DNA metabolic process / nucleotide-activated protein kinase complex / cellular response to L-leucine / Amino acids regulate mTORC1 / triglyceride homeostasis / GDP-dissociation inhibitor activity / positive regulation of lipophagy / cellular oxidant detoxification / regulation of gluconeogenesis / fatty acid beta-oxidation / D-glucose import / positive regulation of macroautophagy / DNA damage response, signal transduction by p53 class mediator / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / response to glucose / cellular response to glucose starvation / negative regulation of TORC1 signaling / protein sequestering activity / positive regulation of TORC1 signaling / cellular response to amino acid starvation / reactive oxygen species metabolic process / TP53 Regulates Metabolic Genes / cellular response to amino acid stimulus / peroxidase activity / response to insulin / regulation of protein phosphorylation / negative regulation of cell growth / 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
Sestrin / PA26 p53-induced protein (sestrin) / AhpD-like
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.004 Å
AuthorsSaxton, R.A. / Knockenhauer, K.E. / Schwartz, T.U.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA10386 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI47389 United States
Department of Defense (DOD, United States)W81XWH-07- 0448 United States
Citation
Journal: Sci.Signal. / Year: 2016
Title: The apo-structure of the leucine sensor Sestrin2 is still elusive.
Authors: Saxton, R.A. / Knockenhauer, K.E. / Schwartz, T.U. / Sabatini, D.M.
#1: Journal: Science / Year: 2016
Title: Structural basis for leucine sensing by the Sestrin2-mTORC1 pathway.
Authors: Saxton, R.A. / Knockenhauer, K.E. / Wolfson, R.L. / Chantranupong, L. / Pacold, M.E. / Wang, T. / Schwartz, T.U. / Sabatini, D.M.
History
DepositionAug 16, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Structure summary
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sestrin-2
B: Sestrin-2
C: Sestrin-2
D: Sestrin-2
E: Sestrin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)273,45910
Polymers272,8035
Non-polymers6565
Water00
1
A: Sestrin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6922
Polymers54,5611
Non-polymers1311
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sestrin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6922
Polymers54,5611
Non-polymers1311
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Sestrin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6922
Polymers54,5611
Non-polymers1311
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Sestrin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6922
Polymers54,5611
Non-polymers1311
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Sestrin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6922
Polymers54,5611
Non-polymers1311
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)292.263, 292.263, 292.263
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein
Sestrin-2 / Hypoxia-induced gene


Mass: 54560.566 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SESN2, Hi95, SEST2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): LoBSTr / References: UniProt: P58004
#2: Chemical
ChemComp-LEU / LEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H13NO2

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.81 Å3/Da / Density % sol: 67.75 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M MES pH 6.0, 1.2 M sodium malonate, 1% (w/v) Jeffamine ED 2001

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3→999 Å / Num. obs: 82209 / % possible obs: 100 % / Redundancy: 40.7 % / Rmerge(I) obs: 0.28 / Net I/σ(I): 19.5
Reflection shellResolution: 3→3.05 Å / Redundancy: 41.9 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 2 / Num. unique all: 4045

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DJ4

5dj4


Resolution: 3.004→103.331 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2254 1637 1.99 %
Rwork0.1888 --
obs0.1895 82205 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.004→103.331 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14603 0 45 0 14648
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115026
X-RAY DIFFRACTIONf_angle_d1.03720363
X-RAY DIFFRACTIONf_dihedral_angle_d15.4618847
X-RAY DIFFRACTIONf_chiral_restr0.0512218
X-RAY DIFFRACTIONf_plane_restr0.0062566
LS refinement shellResolution: 3.004→3.092 Å
RfactorNum. reflection
Rfree0.3207 136
Rwork0.2729 -
obs-6665

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