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- PDB-5cuf: X-ray crystal structure of SeMet human Sestrin2 -

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Basic information

Entry
Database: PDB / ID: 5cuf
TitleX-ray crystal structure of SeMet human Sestrin2
ComponentsSestrin-2
KeywordsOXIDOREDUCTASE / alkylhydroperoxidase
Function / homology
Function and homology information


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
Sestrin / PA26 p53-induced protein (sestrin) / AhpD-like
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.5 Å
AuthorsKim, H. / An, S. / Ro, S.-H. / Lee, J.H. / Cho, U.-S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)2P30-DK020572 United States
Ellison Medical FoundationAG-NS-0932-12 United States
CitationJournal: 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
DepositionJul 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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


Theoretical massNumber of molelcules
Total (without water)277,2125
Polymers277,2125
Non-polymers00
Water00
1
A: Sestrin-2


Theoretical massNumber of molelcules
Total (without water)55,4421
Polymers55,4421
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sestrin-2


Theoretical massNumber of molelcules
Total (without water)55,4421
Polymers55,4421
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Sestrin-2


Theoretical massNumber of molelcules
Total (without water)55,4421
Polymers55,4421
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Sestrin-2


Theoretical massNumber of molelcules
Total (without water)55,4421
Polymers55,4421
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Sestrin-2


Theoretical massNumber of molelcules
Total (without water)55,4421
Polymers55,4421
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)292.680, 292.680, 292.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15B
25C
16B
26D
17B
27E
18C
28D
19C
29E
110D
210E

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

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14AA
24EE
15BB
25CC
16BB
26DD
17BB
27EE
18CC
28DD
19CC
29EE
110DD
210EE

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10

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Components

#1: Protein
Sestrin-2 / Hi95


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
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.79 Å3/Da / Density % sol: 67.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M MES 1.15 M sodium malonate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97879 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 6, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97879 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 3.5→3.59 Å / Redundancy: 3.7 % / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod 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
RfactorNum. reflection% reflectionSelection details
Rfree0.27194 2592 4.9 %RANDOM
Rwork0.23538 ---
obs0.23715 49798 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 103.032 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.5→44.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15032 0 0 0 15032
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01915432
X-RAY DIFFRACTIONr_bond_other_d0.0150.0214393
X-RAY DIFFRACTIONr_angle_refined_deg1.8241.95920907
X-RAY DIFFRACTIONr_angle_other_deg1.888333038
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.75151815
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.16522.895760
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.301152407
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.07515120
X-RAY DIFFRACTIONr_chiral_restr0.0950.22240
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02117210
X-RAY DIFFRACTIONr_gen_planes_other0.0110.023800
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it13.32110.8727350
X-RAY DIFFRACTIONr_mcbond_other13.32110.8737349
X-RAY DIFFRACTIONr_mcangle_it16.6416.4539135
X-RAY DIFFRACTIONr_mcangle_other16.6416.4529136
X-RAY DIFFRACTIONr_scbond_it10.84310.1648082
X-RAY DIFFRACTIONr_scbond_other10.84310.1648083
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other15.34415.44811773
X-RAY DIFFRACTIONr_long_range_B_refined20.02260884
X-RAY DIFFRACTIONr_long_range_B_other20.02260885
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A456840.08
12B456840.08
21A456900.08
22C456900.08
31A455240.08
32D455240.08
41A455760.08
42E455760.08
51B459220.06
52C459220.06
61B459500.06
62D459500.06
71B459700.06
72E459700.06
81C461080.05
82D461080.05
91C460340.05
92E460340.05
101D462500.04
102E462500.04
LS refinement shellResolution: 3.5→3.591 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 204 -
Rwork0.302 3633 -
obs--99.97 %

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