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- PDB-4jsn: structure of mTORdeltaN-mLST8 complex -

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Basic information

Entry
Database: PDB / ID: 4jsn
Titlestructure of mTORdeltaN-mLST8 complex
Components
  • Serine/threonine-protein kinase mTOR
  • Target of rapamycin complex subunit LST8MTOR
KeywordsTRANSFERASE / helical repeat / kinase / wd40 repeat / protein kinase / Raptor
Function / homology
Function and homology information


RNA polymerase III type 2 promoter sequence-specific DNA binding / positive regulation of cytoplasmic translational initiation / RNA polymerase III type 1 promoter sequence-specific DNA binding / positive regulation of pentose-phosphate shunt / T-helper 1 cell lineage commitment / regulation of locomotor rhythm / positive regulation of wound healing, spreading of epidermal cells / cellular response to leucine starvation / TFIIIC-class transcription factor complex binding / TORC2 complex ...RNA polymerase III type 2 promoter sequence-specific DNA binding / positive regulation of cytoplasmic translational initiation / RNA polymerase III type 1 promoter sequence-specific DNA binding / positive regulation of pentose-phosphate shunt / T-helper 1 cell lineage commitment / regulation of locomotor rhythm / positive regulation of wound healing, spreading of epidermal cells / cellular response to leucine starvation / TFIIIC-class transcription factor complex binding / TORC2 complex / heart valve morphogenesis / regulation of membrane permeability / negative regulation of lysosome organization / RNA polymerase III type 3 promoter sequence-specific DNA binding / TORC1 complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / calcineurin-NFAT signaling cascade / regulation of autophagosome assembly / TORC1 signaling / voluntary musculoskeletal movement / regulation of osteoclast differentiation / positive regulation of keratinocyte migration / cellular response to L-leucine / MTOR signalling / Amino acids regulate mTORC1 / cellular response to nutrient / energy reserve metabolic process / Energy dependent regulation of mTOR by LKB1-AMPK / nucleus localization / ruffle organization / negative regulation of cell size / cellular response to osmotic stress / anoikis / cardiac muscle cell development / positive regulation of transcription by RNA polymerase III / negative regulation of protein localization to nucleus / regulation of myelination / negative regulation of calcineurin-NFAT signaling cascade / Macroautophagy / regulation of cell size / negative regulation of macroautophagy / lysosome organization / positive regulation of oligodendrocyte differentiation / positive regulation of actin filament polymerization / positive regulation of myotube differentiation / behavioral response to pain / TOR signaling / oligodendrocyte differentiation / mTORC1-mediated signalling / germ cell development / Constitutive Signaling by AKT1 E17K in Cancer / cellular response to nutrient levels / CD28 dependent PI3K/Akt signaling / positive regulation of phosphoprotein phosphatase activity / positive regulation of translational initiation / neuronal action potential / HSF1-dependent transactivation / positive regulation of TOR signaling / positive regulation of epithelial to mesenchymal transition / regulation of macroautophagy / endomembrane system / 'de novo' pyrimidine nucleobase biosynthetic process / response to amino acid / positive regulation of lipid biosynthetic process / phagocytic vesicle / positive regulation of lamellipodium assembly / heart morphogenesis / regulation of cellular response to heat / cytoskeleton organization / cardiac muscle contraction / positive regulation of stress fiber assembly / cellular response to amino acid starvation / T cell costimulation / cellular response to starvation / positive regulation of glycolytic process / protein serine/threonine kinase activator activity / response to nutrient levels / post-embryonic development / negative regulation of autophagy / response to nutrient / VEGFR2 mediated vascular permeability / positive regulation of translation / regulation of signal transduction by p53 class mediator / Regulation of PTEN gene transcription / regulation of cell growth / regulation of actin cytoskeleton organization / cellular response to amino acid stimulus / TP53 Regulates Metabolic Genes / macroautophagy / phosphoprotein binding / protein catabolic process / protein destabilization / multicellular organism growth / regulation of circadian rhythm / PML body / cellular response to insulin stimulus / rhythmic process / positive regulation of peptidyl-tyrosine phosphorylation / Regulation of TP53 Degradation / ribosome binding
Similarity search - Function
Target of rapamycin complex subunit LST8 / Domain of unknown function DUF3385, target of rapamycin protein / Domain of unknown function (DUF3385) / Domain of unknown function / FKBP12-rapamycin binding domain / Serine/threonine-protein kinase TOR / FKBP12-rapamycin binding domain superfamily / FKBP12-rapamycin binding domain / Rapamycin binding domain / PIK-related kinase, FAT ...Target of rapamycin complex subunit LST8 / Domain of unknown function DUF3385, target of rapamycin protein / Domain of unknown function (DUF3385) / Domain of unknown function / FKBP12-rapamycin binding domain / Serine/threonine-protein kinase TOR / FKBP12-rapamycin binding domain superfamily / FKBP12-rapamycin binding domain / Rapamycin binding domain / PIK-related kinase, FAT / FAT domain / FATC domain / FATC / FATC domain / PIK-related kinase / FAT domain profile. / FATC domain profile. / Quinoprotein alcohol dehydrogenase-like superfamily / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / YVTN repeat-like/Quinoprotein amine dehydrogenase / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / 7 Propeller / Methylamine Dehydrogenase; Chain H / Armadillo-like helical / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
Serine/threonine-protein kinase mTOR / Target of rapamycin complex subunit LST8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3.2 Å
AuthorsPavletich, N.P.
CitationJournal: Nature / Year: 2013
Title: mTOR kinase structure, mechanism and regulation.
Authors: Yang, H. / Rudge, D.G. / Koos, J.D. / Vaidialingam, B. / Yang, H.J. / Pavletich, N.P.
History
DepositionMar 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1May 29, 2013Group: Database references
Revision 1.2Feb 28, 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
B: Serine/threonine-protein kinase mTOR
D: Target of rapamycin complex subunit LST8
A: Serine/threonine-protein kinase mTOR
C: Target of rapamycin complex subunit LST8


Theoretical massNumber of molelcules
Total (without water)341,1214
Polymers341,1214
Non-polymers00
Water0
1
B: Serine/threonine-protein kinase mTOR
D: Target of rapamycin complex subunit LST8


Theoretical massNumber of molelcules
Total (without water)170,5602
Polymers170,5602
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Serine/threonine-protein kinase mTOR
C: Target of rapamycin complex subunit LST8


Theoretical massNumber of molelcules
Total (without water)170,5602
Polymers170,5602
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)139.400, 163.200, 207.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.999973, 0.004092, 0.006138), (0.004081, -0.99999, 0.001783), (0.006145, -0.001758, -0.99998)-69.2967, -32.21088, -104.11333

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Components

#1: Protein Serine/threonine-protein kinase mTOR / FK506-binding protein 12-rapamycin complex-associated protein 1 / FKBP12-rapamycin complex- ...FK506-binding protein 12-rapamycin complex-associated protein 1 / FKBP12-rapamycin complex-associated protein / Mammalian target of rapamycin / mTOR / Mechanistic target of rapamycin / Rapamycin and FKBP12 target 1 / Rapamycin target protein 1


Mass: 134650.250 Da / Num. of mol.: 2 / Fragment: FAT FRB KINASE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FRAP, FRAP1, FRAP2, MTOR, RAFT1, RAPT1 / Plasmid: pcDNA 3.1 (+) hygromycine / Cell line (production host): 293F / Production host: Homo Sapiens (human)
References: UniProt: P42345, non-specific serine/threonine protein kinase
#2: Protein Target of rapamycin complex subunit LST8 / MTOR / TORC subunit LST8 / G protein beta subunit-like / Gable / Protein GbetaL / Mammalian lethal with ...TORC subunit LST8 / G protein beta subunit-like / Gable / Protein GbetaL / Mammalian lethal with SEC13 protein 8 / mLST8


Mass: 35910.090 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GBL, LST8, MLST8 / Plasmid: pcDNA 3.1 (+) Zoecine / Cell line (production host): 293F / Production host: Homo sapiens (human) / References: UniProt: Q9BVC4

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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: 3.46 Å3/Da / Density % sol: 64.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris, pH 8.5, 6-8% PEG 8000, 500 mM NaCl, 10 % (v/v) Glycerol, 10 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97925 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97925 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. all: 78795 / Num. obs: 75486 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.107 / Net I/σ(I): 11.3
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.538 / % possible all: 79.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
REFMAC5.7.0032refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 3.2→29.86 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.912 / SU B: 45.13 / SU ML: 0.37 / Cross valid method: THROUGHOUT / ESU R Free: 0.499 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2559 1699 2.5 %RANDOM
Rwork0.21496 ---
obs0.21601 66654 86.61 %-
all-76958 --
Solvent computationIon probe radii: 1.1 Å / Shrinkage radii: 1.1 Å / VDW probe radii: 1.3 Å / Solvent model: MASK
Displacement parametersBiso mean: 87.409 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å20 Å20 Å2
2---1.75 Å2-0 Å2
3---2.47 Å2
Refinement stepCycle: LAST / Resolution: 3.2→29.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22097 0 0 0 22097
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01922605
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.711.94130644
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.34952737
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.75623.9541085
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.145153985
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.98315158
X-RAY DIFFRACTIONr_chiral_restr0.1160.23366
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02117086
X-RAY DIFFRACTIONr_gen_planes_other
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_it2.3441.35710975
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.0473.04813703
X-RAY DIFFRACTIONr_scbond_it2.8881.4511628
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.2→3.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 77 -
Rwork0.334 3206 -
obs--58.01 %
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)
16.5984.1407-0.47278.5908-3.34094.3870.3036-1.05130.03840.9113-0.57180.3173-0.32660.47650.26810.97250.0133-0.00620.9658-0.21780.5853-10.122-5.105-32.943
26.4386-0.29561.02514.3037-5.30776.7097-0.1031-0.23280.8937-0.2243-0.2958-0.19060.12090.6280.39891.37990.0044-0.06331.1769-0.11511.001316.3661.666-25.856
32.6807-1.2991-2.0072.62551.82163.71190.0924-0.02750.03430.3696-0.25950.76820.0912-0.70050.16710.9753-0.06540.02471.2361-0.15330.721512.888-16.685-12.642
44.85722.19651.29972.16421.00721.03310.03890.2429-0.1016-0.03430.0957-0.31530.15890.3073-0.13460.31770.05930.05720.24620.02470.208316.317-44.801-49.817
50.89990.4202-3.20140.9422-1.684214.33420.04370.4280.0861-0.8960.1031-0.1678-0.28920.0585-0.14671.3555-0.0654-0.12651.06340.13150.8454-27.128-43.822-84.239
60.9777-0.05120.07993.4116-1.01570.33620.04190.035-0.1362-0.1067-0.01380.19740.0865-0.0423-0.02810.2433-0.03840.01350.2794-0.0050.1297-13.299-27.38-54.101
76.501-4.46771.10088.6272-3.84434.07350.13960.85790.043-0.9144-0.5566-0.22530.4090.55230.41710.9681-0.04020.08091.0075-0.13540.747859.757-26.98-70.714
85.93581.6794-1.50824.0675-4.17854.3442-0.19540.6711-0.77760.1667-0.1433-0.38090.03180.28190.33861.33480.09780.12721.2811-0.02051.176186.098-33.672-78.023
91.3121-0.61341.16540.3818-0.57871.2497-0.04840.1510.1295-0.2853-0.0270.17160.0258-0.46030.07541.537-0.1019-0.06961.7013-0.09471.503382.358-15.148-91.007
104.3046-2.339-0.9252.60340.84150.8984-0.013-0.26070.08080.04330.066-0.078-0.12750.2856-0.0530.3473-0.0764-0.02150.29470.02950.547285.85413.152-54.337
110.1054-0.06610.54010.235-1.10289.030.2007-0.2179-0.07440.30710.2363-0.00230.12480.3551-0.4371.75650.37730.31481.60880.2871.861342.60811.913-20.027
120.9880.2837-0.03893.7397-1.20290.4090.0116-0.04260.32610.17160.05760.174-0.1216-0.0293-0.06920.24320.04610.06190.3088-0.01940.544956.403-4.42-49.939
132.764-0.16140.60533.92530.85893.6663-0.05790.5053-0.0322-0.4990.0936-0.076-0.05810.0455-0.03580.3099-0.0290.00690.22210.00380.0031-1.9569.425-79.222
142.9592-0.0767-0.89443.96020.22783.205-0.0663-0.8570.04810.76560.0837-0.4569-0.04260.1153-0.01740.41620.02-0.13970.45540.03330.49867.759-40.96-24.174
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B1385 - 1442
2X-RAY DIFFRACTION2B1443 - 1504
3X-RAY DIFFRACTION3B1505 - 1678
4X-RAY DIFFRACTION4B1679 - 2021
5X-RAY DIFFRACTION5B2022 - 2115
6X-RAY DIFFRACTION6B2116 - 2459
7X-RAY DIFFRACTION7A1385 - 1442
8X-RAY DIFFRACTION8A1443 - 1504
9X-RAY DIFFRACTION9A1505 - 1678
10X-RAY DIFFRACTION10A1679 - 2021
11X-RAY DIFFRACTION11A2022 - 2115
12X-RAY DIFFRACTION12A2116 - 2459
13X-RAY DIFFRACTION13D8 - 324
14X-RAY DIFFRACTION14C8 - 324

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