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- PDB-4jt6: structure of mTORDeltaN-mLST8-PI-103 complex -

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Basic information

Entry
Database: PDB / ID: 4jt6
Titlestructure of mTORDeltaN-mLST8-PI-103 complex
Components
  • mLST8
  • mTOR
Keywordstransferase/transferase inhibitor / kinase / transferase / transferase-transferase inhibitor complex
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 / protein serine/threonine kinase activator activity / positive regulation of glycolytic process / negative regulation of autophagy / response to nutrient levels / post-embryonic development / response to nutrient / positive regulation of translation / VEGFR2 mediated vascular permeability / 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 / multicellular organism growth / protein destabilization / 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
Chem-X6K / 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: 3.6 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: mTOR
D: mLST8
A: mTOR
C: mLST8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)341,8176
Polymers341,1214
Non-polymers6972
Water0
1
B: mTOR
D: mLST8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,9093
Polymers170,5602
Non-polymers3481
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: mTOR
C: mLST8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,9093
Polymers170,5602
Non-polymers3481
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.)90.000, 90.000, 90.000
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
18
DetailsThe biological unit is a heterodimer. There are 2 biological units in the asymmetric unit (chains A & C and chains B & D)

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Components

#1: Protein mTOR /


Mass: 134650.250 Da / Num. of mol.: 2 / Fragment: unp residues 1376-2549
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: mTOR / Plasmid: pcDNA3.1(+)hygromycin / Cell line (production host): HEK293 / Production host: Homo Sapiens (human) / References: UniProt: P42345
#2: Protein mLST8 /


Mass: 35910.090 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: mLST8 / Plasmid: pcDNA3.1(+)blasticidin / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q9BVC4
#3: Chemical ChemComp-X6K / 3-(4-MORPHOLIN-4-YLPYRIDO[3',2':4,5]FURO[3,2-D]PYRIMIDIN-2-YL)PHENOL / PI-103


Mass: 348.355 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H16N4O3

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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, hanging drop vapor diffusion, temperature 277K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / 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: 3.6→40 Å / Num. all: 55940 / Num. obs: 49787 / % possible obs: 89 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allDiffraction-ID% possible all
3.6-3.732.50.654257176.9
3.73-3.882.50.5644325178.5
3.88-4.052.60.4054451180.3
4.05-4.272.80.3544811187.3
4.27-4.532.90.2744863187.6
4.53-4.883.20.2455134192.2
4.88-5.373.50.2695215193.3
5.37-6.153.80.3115368195.7
6.15-7.744.10.2185564198.2
7.74-4040.065799198.5

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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: 3.6→39.67 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.848 / Occupancy max: 1 / Occupancy min: 1 / SU B: 36.422 / SU ML: 0.517 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.808 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2749 1294 3.1 %RANDOM
Rwork0.2386 ---
all0.2397 55756 --
obs0.2397 42196 75.68 %-
Solvent computationIon probe radii: 1.1 Å / Shrinkage radii: 1.1 Å / VDW probe radii: 1.3 Å / Solvent model: MASK
Displacement parametersBiso max: 500 Å2 / Biso mean: 65.5774 Å2 / Biso min: 21.51 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å20 Å20 Å2
2---2.17 Å2-0 Å2
3---2.8 Å2
Refinement stepCycle: LAST / Resolution: 3.6→39.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22097 0 52 0 22149
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01922698
X-RAY DIFFRACTIONr_angle_refined_deg1.2171.94430778
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.40652742
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.3723.9521088
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.42153982
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.63815158
X-RAY DIFFRACTIONr_chiral_restr0.0890.23368
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02117176
X-RAY DIFFRACTIONr_mcbond_it1.4753.24510990
X-RAY DIFFRACTIONr_mcangle_it2.7277.29613723
X-RAY DIFFRACTIONr_scbond_it1.0683.29911706
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 THERMAL4.1799
1B223MEDIUM THERMAL4.7199
2B271MEDIUM POSITIONAL0.010.5
2B248TIGHT THERMAL9.599
2B271MEDIUM THERMAL9.899
3B121MEDIUM POSITIONAL0.020.5
3B132TIGHT THERMAL9.899
3B121MEDIUM THERMAL9.7899
4B161MEDIUM POSITIONAL0.020.5
4B172TIGHT THERMAL18.7299
4B161MEDIUM THERMAL18.399
5B211MEDIUM POSITIONAL0.030.5
5B188TIGHT THERMAL28.7799
5B211MEDIUM THERMAL25.2899
6B204MEDIUM POSITIONAL0.020.5
6B204TIGHT THERMAL12.899
6B204MEDIUM THERMAL12.5799
7B238MEDIUM POSITIONAL0.020.5
7B224TIGHT THERMAL3.3999
7B238MEDIUM THERMAL3.4999
8B363MEDIUM POSITIONAL0.020.5
8B320TIGHT THERMAL3.6399
8B363MEDIUM THERMAL4.3199
9B258MEDIUM POSITIONAL0.020.5
9B256TIGHT THERMAL4.6999
9B258MEDIUM THERMAL4.8299
10B283MEDIUM POSITIONAL0.020.5
10B284TIGHT THERMAL5.6499
10B283MEDIUM THERMAL5.9899
11B73MEDIUM POSITIONAL0.020.5
11B80TIGHT THERMAL6.8999
11B73MEDIUM THERMAL6.8699
12B425MEDIUM POSITIONAL0.020.5
12B376TIGHT THERMAL17.0199
12B425MEDIUM THERMAL16.7699
13B293MEDIUM POSITIONAL0.050.5
13B300TIGHT THERMAL9.1499
13B293MEDIUM THERMAL9.4199
14B90MEDIUM POSITIONAL0.020.5
14B88TIGHT THERMAL5.0999
14B90MEDIUM THERMAL6.0899
15B108MEDIUM POSITIONAL0.020.5
15B116TIGHT THERMAL1.8899
15B108MEDIUM THERMAL2.0699
16B1055MEDIUM POSITIONAL0.020.5
16B1012TIGHT THERMAL4.0599
16B1055MEDIUM THERMAL4.2399
17D1186MEDIUM POSITIONAL0.020.5
17D1268TIGHT THERMAL9.9599
17D1186MEDIUM THERMAL10.4599
LS refinement shellResolution: 3.6→3.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 65 -
Rwork0.368 2188 -
all-2253 -
obs--55.66 %

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