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- PDB-5dj4: Leucine-bound Sestrin2 from Homo sapiens -

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Basic information

Entry
Database: PDB / ID: 5dj4
TitleLeucine-bound Sestrin2 from Homo sapiens
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 / 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
Sestrin / PA26 p53-induced protein (sestrin) / AhpD-like
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.697 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)(R01CA103866 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
CitationJournal: 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
DepositionSep 1, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2015Group: Database references
Revision 1.2Jan 13, 2016Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Apr 10, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
Water2,072115
1
A: Sestrin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6922
Polymers54,5611
Non-polymers1311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sestrin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6922
Polymers54,5611
Non-polymers1311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Sestrin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6922
Polymers54,5611
Non-polymers1311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Sestrin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6922
Polymers54,5611
Non-polymers1311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Sestrin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6922
Polymers54,5611
Non-polymers1311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
A: Sestrin-2
hetero molecules

A: Sestrin-2
hetero molecules

A: Sestrin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,0756
Polymers163,6823
Non-polymers3943
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_665-z+1,-x+1,y1
crystal symmetry operation10_656-y+1,z,-x+11
Buried area4670 Å2
ΔGint-28 kcal/mol
Surface area42690 Å2
MethodPISA
7
B: Sestrin-2
hetero molecules

B: Sestrin-2
hetero molecules

B: Sestrin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,0756
Polymers163,6823
Non-polymers3943
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area4550 Å2
ΔGint-28 kcal/mol
Surface area42750 Å2
MethodPISA
8
C: Sestrin-2
hetero molecules

D: Sestrin-2
hetero molecules

E: Sestrin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,0756
Polymers163,6823
Non-polymers3943
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation10_656-y+1,z,-x+11
Buried area4610 Å2
ΔGint-27 kcal/mol
Surface area42750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)293.029, 293.029, 293.029
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 / SESN2 / Hi95


Mass: 54560.566 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) / Strain (production host): BL21 (DE3) / Variant (production host): LOBSTR / References: UniProt: P58004
#2: Chemical
ChemComp-LEU / LEUCINE / Leucine


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H13NO2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O

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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: 3.84 Å3/Da / Density % sol: 67.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1.2 M disodium malonate, 0.1 M MES pH 6.0, 1% (v/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: 2.7→92.67 Å / Num. obs: 114283 / % possible obs: 100 % / Redundancy: 40 % / Net I/σ(I): 24.47
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 39.4 % / Rsym value: 15.3 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.697→92.664 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2226 2001 1.75 %
Rwork0.1964 --
obs0.1969 114265 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.697→92.664 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14751 0 45 115 14911
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01115210
X-RAY DIFFRACTIONf_angle_d1.0920601
X-RAY DIFFRACTIONf_dihedral_angle_d18.0795509
X-RAY DIFFRACTIONf_chiral_restr0.0542230
X-RAY DIFFRACTIONf_plane_restr0.0042606
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6969-2.76430.29541400.27137980X-RAY DIFFRACTION100
2.7643-2.83910.28891410.26717948X-RAY DIFFRACTION100
2.8391-2.92260.32861400.26197967X-RAY DIFFRACTION100
2.9226-3.01690.3011440.25558022X-RAY DIFFRACTION100
3.0169-3.12480.27231420.24027934X-RAY DIFFRACTION100
3.1248-3.24990.26931470.23237989X-RAY DIFFRACTION100
3.2499-3.39780.25031420.22898006X-RAY DIFFRACTION100
3.3978-3.5770.24381460.21287982X-RAY DIFFRACTION100
3.577-3.80110.23351450.18497999X-RAY DIFFRACTION100
3.8011-4.09450.1961410.1698040X-RAY DIFFRACTION100
4.0945-4.50660.19181430.15878009X-RAY DIFFRACTION100
4.5066-5.15870.17651440.168040X-RAY DIFFRACTION100
5.1587-6.49910.21861380.20468109X-RAY DIFFRACTION100
6.4991-92.71860.19921480.18618239X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.17150.51560.11921.5001-0.13821.2829-0.04960.03890.0998-0.08390.0226-0.0452-0.0804-0.00790.04740.42420.0431-0.00750.42530.00330.5002193.732980.790471.5174
22.20870.58750.26331.9390.20422.2447-0.036-0.24320.1730.00490.01010.6544-0.1053-0.58480.04610.50560.10630.04830.7687-0.00710.8066172.693878.837377.3029
32.62290.1417-0.52011.82140.26993.43380.0012-0.1784-0.14810.02540.02710.34410.1686-0.4446-0.02490.39440.0005-0.00140.54310.03830.5555177.925270.854278.3116
41.9909-0.3295-0.54741.6916-0.19831.0210.01270.01780.01070.0698-0.0060.1135-0.0656-0.065-0.01120.44930.013-0.03640.4541-0.01460.366291.189567.728792.8264
51.6163-0.73340.08522.4748-0.05071.3158-0.1857-0.34280.03250.54040.1366-0.53480.18960.39540.02190.66390.0167-0.11840.86060.020.6367111.77564.1037100.2087
62.94350.63640.11382.5374-0.07692.1873-0.0592-0.0556-0.09210.09860.0001-0.40180.14140.45420.07110.40540.0583-0.02810.51630.03940.4422110.420263.241790.6402
71.59260.57890.89841.11450.13342.51080.10980.1386-0.1447-0.00960.0858-0.16190.1160.2097-0.17890.5565-0.04170.03840.5997-0.05990.4821188.945646.0144126.8912
81.5708-0.1623-0.99112.0487-0.0683.16460.08930.36370.0529-0.44780.05820.0031-0.419-0.1237-0.15270.7068-0.05070.02230.79120.03220.6235177.080256.7305111.4969
92.8744-0.73330.23212.44540.04382.64140.03180.4347-0.1555-0.3180.09010.15370.1894-0.3176-0.12670.5812-0.11220.02880.7033-0.0010.4705173.578847.9514114.4225
101.3138-0.49240.33961.096-0.06711.608-0.0029-0.0108-0.00070.2258-0.07740.20610.1715-0.2060.10730.50910.01820.0230.7266-0.08430.5071118.254443.3521135.9258
113.0774-0.5381-0.42782.13160.17831.8132-0.0520.00620.22910.02560.0843-0.47890.02530.6981-0.04940.6126-0.0245-0.0430.871-0.00530.6711139.348647.7012126.9019
122.0544-0.2178-0.71773.1846-0.51052.6806-0.04790.4876-0.1409-0.1739-0.0275-0.13570.23420.26310.06810.45970.0267-0.02470.7838-0.06630.4891131.665143.202122.0147
131.2186-0.2363-0.18932.6725-0.8361.20980.00640.02930.0421-0.3993-0.0110.21320.0903-0.08790.01430.47510.0009-0.00240.4746-0.02230.6787133.311693.616550.0176
142.41080.8134-0.33742.0312-0.02161.84780.0824-0.3614-0.05880.2043-0.15610.52210.1707-0.21250.08190.56860.0030.07270.74440.02870.8557131.937483.768769.2132
152.18250.57340.63852.2347-0.25053.09470.0132-0.2173-0.3564-0.1045-0.0673-0.01060.3360.08280.06060.42540.03310.06520.48230.02850.7094138.924679.966463.4137
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 66 through 213 )
2X-RAY DIFFRACTION2chain 'A' and (resid 214 through 338)
3X-RAY DIFFRACTION3chain 'A' and (resid 339 through 501 )
4X-RAY DIFFRACTION4chain 'B' and (resid 66 through 213 )
5X-RAY DIFFRACTION5chain 'B' and (resid 214 through 338)
6X-RAY DIFFRACTION6chain 'B' and (resid 339 through 501 )
7X-RAY DIFFRACTION7chain 'C' and (resid 66 through 213 )
8X-RAY DIFFRACTION8chain 'C' and (resid 214 through 338 )
9X-RAY DIFFRACTION9chain 'C' and (resid 339 through 501)
10X-RAY DIFFRACTION10chain 'D' and (resid 66 through 123 )
11X-RAY DIFFRACTION11chain 'D' and (resid 214 through 338 )
12X-RAY DIFFRACTION12chain 'D' and (resid 339 through 501 )
13X-RAY DIFFRACTION13chain 'E' and (resid 66 through 213)
14X-RAY DIFFRACTION14chain 'E' and (resid 214 through 338 )
15X-RAY DIFFRACTION15chain 'E' and (resid 339 through 501 )

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