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- PDB-6n0m: CRYSTAL STRUCTURE OF SESTRIN2 IN COMPLEX WITH NV-0005138 -

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Basic information

Entry
Database: PDB / ID: 6n0m
TitleCRYSTAL STRUCTURE OF SESTRIN2 IN COMPLEX WITH NV-0005138
ComponentsSestrin-2SESN2
KeywordsSIGNALING PROTEIN / MTOR / LEUCINE / AMINO-ACID / SENSING
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 / PH domain binding / regulation of TORC1 signaling / oxidoreductase activity, acting on peroxide as acceptor / cellular response to leucine starvation / TORC2 complex ...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 / PH domain binding / regulation of TORC1 signaling / oxidoreductase activity, acting on peroxide as acceptor / cellular response to leucine starvation / TORC2 complex / 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 / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / 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 / 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 / peroxidase activity / protein sequestering activity / phosphatidylinositol 3-kinase/protein kinase B signal transduction / cellular response to amino acid stimulus / TP53 Regulates Metabolic Genes / 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
Sestrin / PA26 p53-induced protein (sestrin) / AhpD-like
Similarity search - Domain/homology
4-(difluoromethyl)-L-leucine / Sestrin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsO'Neill, D.
CitationJournal: Sci Rep / Year: 2019
Title: Discovery of NV-5138, the first selective Brain mTORC1 activator.
Authors: Sengupta, S. / Giaime, E. / Narayan, S. / Hahm, S. / Howell, J. / O'Neill, D. / Vlasuk, G.P. / Saiah, E.
History
DepositionNov 7, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 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)238,20010
Polymers237,2945
Non-polymers9065
Water0
1
A: Sestrin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6402
Polymers47,4591
Non-polymers1811
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sestrin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6402
Polymers47,4591
Non-polymers1811
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Sestrin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6402
Polymers47,4591
Non-polymers1811
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Sestrin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6402
Polymers47,4591
Non-polymers1811
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Sestrin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6402
Polymers47,4591
Non-polymers1811
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)290.410, 290.410, 290.410
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23

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Components

#1: Protein
Sestrin-2 / SESN2 / Hypoxia-induced gene


Mass: 47458.730 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 BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P58004, peroxiredoxin
#2: Chemical
ChemComp-K94 / 4-(difluoromethyl)-L-leucine / NV-5138


Mass: 181.180 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C7H13F2NO2 / Feature type: SUBJECT OF INVESTIGATION

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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: 4.38 Å3/Da / Density % sol: 71.9 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 1.35M Na malonate pH 6.5, 0.1M Mes pH 6.0 / PH range: 6-6.5

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.98→48.4 Å / Num. obs: 82533 / % possible obs: 99.8 % / Redundancy: 23 % / Rmerge(I) obs: 0.53 / Net I/σ(I): 8.2
Reflection shellResolution: 2.98→3.06 Å / Mean I/σ(I) obs: 0.29 / CC1/2: 0.223 / Rrim(I) all: 0.543 / % possible all: 99.3

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Processing

Software
NameVersionClassification
XDSdata reduction
REFMAC5.8.0103refinement
PDB_EXTRACT3.24data extraction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DJ4

5dj4


Resolution: 3.3→48.4 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.918 / SU B: 21.599 / SU ML: 0.337 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.425
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2502 3046 5 %RANDOM
Rwork0.1836 ---
obs0.1869 57875 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 218.53 Å2 / Biso mean: 107.251 Å2 / Biso min: 65.47 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 3.3→48.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14751 0 60 0 14811
Biso mean--100.86 --
Num. residues----1824
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01915191
X-RAY DIFFRACTIONr_bond_other_d0.0020.0214182
X-RAY DIFFRACTIONr_angle_refined_deg1.6071.95120589
X-RAY DIFFRACTIONr_angle_other_deg1.017332488
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.39451799
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.15822.814725
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.519152508
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.80815113
X-RAY DIFFRACTIONr_chiral_restr0.0840.22234
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216949
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023744
LS refinement shellResolution: 3.3→3.385 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 222 -
Rwork0.349 4222 -
all-4444 -
obs--99.93 %

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