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- PDB-4jt5: mTORdeltaN-mLST8-pp242 complex -

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Basic information

Entry
Database: PDB / ID: 4jt5
TitlemTORdeltaN-mLST8-pp242 complex
Components
  • Serine/threonine-protein kinase mTOR
  • Target of rapamycin complex subunit LST8
Keywordstransferase/transferase inhibitor / kinase / transferase-transferase inhibitor complex
Function / homology
Function and homology information


RNA polymerase III type 2 promoter sequence-specific DNA binding / RNA polymerase III type 1 promoter sequence-specific DNA binding / positive regulation of cytoplasmic translational initiation / regulation of locomotor rhythm / T-helper 1 cell lineage commitment / positive regulation of pentose-phosphate shunt / positive regulation of wound healing, spreading of epidermal cells / TORC2 signaling / TORC2 complex / regulation of membrane permeability ...RNA polymerase III type 2 promoter sequence-specific DNA binding / RNA polymerase III type 1 promoter sequence-specific DNA binding / positive regulation of cytoplasmic translational initiation / regulation of locomotor rhythm / T-helper 1 cell lineage commitment / positive regulation of pentose-phosphate shunt / positive regulation of wound healing, spreading of epidermal cells / TORC2 signaling / TORC2 complex / regulation of membrane permeability / cellular response to leucine starvation / negative regulation of lysosome organization / heart valve morphogenesis / TFIIIC-class transcription factor complex binding / TORC1 complex / voluntary musculoskeletal movement / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / calcineurin-NFAT signaling cascade / RNA polymerase III type 3 promoter sequence-specific DNA binding / positive regulation of keratinocyte migration / regulation of osteoclast differentiation / regulation of lysosome organization / MTOR signalling / cellular response to nutrient / cellular response to L-leucine / energy reserve metabolic process / Amino acids regulate mTORC1 / regulation of autophagosome assembly / Energy dependent regulation of mTOR by LKB1-AMPK / TORC1 signaling / ruffle organization / serine/threonine protein kinase complex / cellular response to methionine / negative regulation of cell size / positive regulation of ubiquitin-dependent protein catabolic process / cellular response to osmotic stress / negative regulation of protein localization to nucleus / anoikis / inositol hexakisphosphate binding / cardiac muscle cell development / negative regulation of calcineurin-NFAT signaling cascade / regulation of myelination / positive regulation of transcription by RNA polymerase III / negative regulation of macroautophagy / Macroautophagy / positive regulation of myotube differentiation / regulation of cell size / Constitutive Signaling by AKT1 E17K in Cancer / positive regulation of actin filament polymerization / germ cell development / TOR signaling / behavioral response to pain / mTORC1-mediated signalling / oligodendrocyte differentiation / positive regulation of oligodendrocyte differentiation / positive regulation of translational initiation / CD28 dependent PI3K/Akt signaling / HSF1-dependent transactivation / positive regulation of TOR signaling / regulation of macroautophagy / response to amino acid / 'de novo' pyrimidine nucleobase biosynthetic process / positive regulation of epithelial to mesenchymal transition / vascular endothelial cell response to laminar fluid shear stress / positive regulation of lipid biosynthetic process / heart morphogenesis / cellular response to nutrient levels / neuronal action potential / regulation of cellular response to heat / positive regulation of lamellipodium assembly / cardiac muscle contraction / phagocytic vesicle / T cell costimulation / positive regulation of stress fiber assembly / cytoskeleton organization / endomembrane system / negative regulation of insulin receptor signaling pathway / negative regulation of autophagy / cellular response to amino acid starvation / positive regulation of translation / regulation of signal transduction by p53 class mediator / positive regulation of glycolytic process / cellular response to starvation / protein serine/threonine kinase activator activity / Regulation of PTEN gene transcription / VEGFR2 mediated vascular permeability / post-embryonic development / TP53 Regulates Metabolic Genes / regulation of actin cytoskeleton organization / cellular response to amino acid stimulus / non-specific protein-tyrosine kinase / macroautophagy / phosphoprotein binding / response to nutrient levels / regulation of cell growth / regulation of circadian rhythm / PML body / protein destabilization / response to virus / multicellular organism growth
Similarity search - Function
Target of rapamycin complex subunit LST8 / Domain of unknown function DUF3385, target of rapamycin protein / Serine/threonine-protein kinase mTOR domain / 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 / Serine/threonine-protein kinase ATR-like, HEAT repeats ...Target of rapamycin complex subunit LST8 / Domain of unknown function DUF3385, target of rapamycin protein / Serine/threonine-protein kinase mTOR domain / 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 / Serine/threonine-protein kinase ATR-like, HEAT repeats / : / FATC domain / PIK-related kinase, FAT / FAT 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. / 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 / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Armadillo-like helical / Tetratricopeptide-like helical domain superfamily / WD domain, G-beta repeat / Armadillo-type fold / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
Chem-P2X / Serine/threonine-protein kinase mTOR / Target of rapamycin complex subunit LST8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.45 Å
AuthorsPavletich, N.P. / Yang, H.
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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)341,7376
Polymers341,1214
Non-polymers6172
Water00
1
B: Serine/threonine-protein kinase mTOR
D: Target of rapamycin complex subunit LST8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,8693
Polymers170,5602
Non-polymers3081
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Serine/threonine-protein kinase mTOR
C: Target of rapamycin complex subunit LST8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,8693
Polymers170,5602
Non-polymers3081
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 domain:
IDEns-IDDetails
11B
21A
12B
22A
13B
23A
14B
24A
15B
25A
16B
26A
17B
27A
18B
28A
19B
29A
110B
210A
111B
211A
112B
212A
113B
213A
114B
214A
115B
215A
116B
216A
117D
217C

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17

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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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FRAP, FRAP1, FRAP2, MTOR, RAFT1, RAPT1 / Plasmid: pcDNA3.1(+)hygromycin / Cell line (production host): HEK293 / Production host: Homo Sapiens (human)
References: UniProt: P42345, non-specific serine/threonine protein kinase
#2: Protein Target of rapamycin complex subunit LST8 / 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: pcDNA3.1(+)blasticidin / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q9BVC4
#3: Chemical ChemComp-P2X / 2-[4-amino-1-(propan-2-yl)-1H-pyrazolo[3,4-d]pyrimidin-3-yl]-1H-indol-5-ol


Mass: 308.338 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H16N6O

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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: PEG 8000, NaCl , pH 8.5, 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: 0.97918 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: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.45→40 Å / Num. all: 63608 / Num. obs: 61700 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
3.45-3.572.70.629191.2
3.57-3.723.30.563193.7
3.72-3.893.80.441197.5
3.89-4.093.70.279197
4.09-4.354.10.205199.2
4.35-4.684.10.15199.1
4.68-5.154.10.136198.8
5.15-5.894.10.163198.6
5.89-7.4240.13197.9
7.42-403.80.043196.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
REFMAC5.7.0032refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.45→39.67 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.875 / Occupancy max: 1 / Occupancy min: 1 / SU B: 31.708 / SU ML: 0.468 / Cross valid method: THROUGHOUT / ESU R Free: 0.645 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.27104 1639 3 %RANDOM
Rwork0.23313 ---
obs0.23428 52634 85.84 %-
all-63225 --
Solvent computationIon probe radii: 1.1 Å / Shrinkage radii: 1.1 Å / VDW probe radii: 1.3 Å / Solvent model: MASK
Displacement parametersBiso mean: 68.406 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å2-0 Å20 Å2
2---2.02 Å2-0 Å2
3---1.96 Å2
Refinement stepCycle: LAST / Resolution: 3.45→39.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22097 0 46 0 22143
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01922657
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2591.94430722
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.58252737
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.05923.9541085
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.023153985
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.23815158
X-RAY DIFFRACTIONr_chiral_restr0.0930.23368
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02117132
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_it1.7273.37810975
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.1547.59513703
X-RAY DIFFRACTIONr_scbond_it1.513.44711681
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1B284TIGHT POSITIONAL0.020.05
1B80TIGHT POSITIONAL0.020.05
1B376TIGHT POSITIONAL0.010.05
1B300TIGHT POSITIONAL0.020.05
1B88TIGHT POSITIONAL0.020.05
1B116TIGHT POSITIONAL0.020.05
1B1012TIGHT POSITIONAL0.020.05
1B1268TIGHT POSITIONAL0.020.05
1B223MEDIUM POSITIONAL0.020.5
1B232TIGHT THERMAL2.8299
1B223MEDIUM THERMAL3.6599
2B271MEDIUM POSITIONAL0.020.5
2B248TIGHT THERMAL5.7999
2B271MEDIUM THERMAL6.3699
3B121MEDIUM POSITIONAL0.020.5
3B132TIGHT THERMAL5.0499
3B121MEDIUM THERMAL6.5699
4B161MEDIUM POSITIONAL0.020.5
4B172TIGHT THERMAL12.0399
4B161MEDIUM THERMAL11.9299
5B211MEDIUM POSITIONAL0.030.5
5B188TIGHT THERMAL25.8399
5B211MEDIUM THERMAL24.6799
6B204MEDIUM POSITIONAL0.020.5
6B204TIGHT THERMAL13.7999
6B204MEDIUM THERMAL14.2699
7B238MEDIUM POSITIONAL0.020.5
7B224TIGHT THERMAL4.2699
7B238MEDIUM THERMAL499
8B363MEDIUM POSITIONAL0.020.5
8B320TIGHT THERMAL2.9599
8B363MEDIUM THERMAL3.8799
9B258MEDIUM POSITIONAL0.030.5
9B256TIGHT THERMAL5.1399
9B258MEDIUM THERMAL5.4699
10B283MEDIUM POSITIONAL0.030.5
10B284TIGHT THERMAL6.5399
10B283MEDIUM THERMAL6.6199
11B73MEDIUM POSITIONAL0.030.5
11B80TIGHT THERMAL6.8499
11B73MEDIUM THERMAL6.7999
12B425MEDIUM POSITIONAL0.020.5
12B376TIGHT THERMAL21.1799
12B425MEDIUM THERMAL20.7199
13B293MEDIUM POSITIONAL0.020.5
13B300TIGHT THERMAL6.7299
13B293MEDIUM THERMAL799
14B90MEDIUM POSITIONAL0.030.5
14B88TIGHT THERMAL4.2299
14B90MEDIUM THERMAL4.9599
15B108MEDIUM POSITIONAL0.020.5
15B116TIGHT THERMAL4.1599
15B108MEDIUM THERMAL4.3399
16B1055MEDIUM POSITIONAL0.030.5
16B1012TIGHT THERMAL3.9899
16B1055MEDIUM THERMAL4.0799
17D1186MEDIUM POSITIONAL0.020.5
17D1268TIGHT THERMAL10.7899
17D1186MEDIUM THERMAL11.1599
LS refinement shellResolution: 3.45→3.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 83 -
Rwork0.341 3094 -
obs--69.49 %

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