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- PDB-4jsp: structure of mTORDeltaN-mLST8-ATPgammaS-Mg complex -

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Basic information

Entry
Database: PDB / ID: 4jsp
Titlestructure of mTORDeltaN-mLST8-ATPgammaS-Mg complex
Components
  • Serine/threonine-protein kinase mTOR
  • Target of rapamycin complex subunit LST8MTOR
KeywordsTRANSFERASE / Kinase
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 / response to nutrient / negative regulation of autophagy / positive regulation of translation / VEGFR2 mediated vascular permeability / Regulation of PTEN gene transcription / regulation of signal transduction by p53 class mediator / 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
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Serine/threonine-protein kinase mTOR / Target of rapamycin complex subunit LST8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3.3 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 1, 2013Provider: repository / Type: Initial release
Revision 1.1May 8, 2013Group: Structure summary
Revision 1.2May 29, 2013Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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)342,26410
Polymers341,1214
Non-polymers1,1446
Water0
1
B: Serine/threonine-protein kinase mTOR
D: Target of rapamycin complex subunit LST8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,1325
Polymers170,5602
Non-polymers5723
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)171,1325
Polymers170,5602
Non-polymers5723
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

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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: unp residues 1376-2549
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 / 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: pcDNA3.1(+)blasticidin / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human) / References: UniProt: Q9BVC4
#3: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg

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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: 0.97925 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: 3.3→100 Å / Num. obs: 70381 / % possible obs: 98.5 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.149 / Χ2: 0.729 / Net I/σ(I): 4.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.3-3.422.50.61267170.822195.2
3.42-3.553.20.45168050.862196.4
3.55-3.724.40.43370250.88199.4
3.72-3.914.60.32670270.865199.5
3.91-4.164.80.2270540.731199.7
4.16-4.484.70.14470970.681199.6
4.48-4.934.90.10970230.661198.9
4.93-5.645.10.11671800.661199.9
5.64-7.114.70.09771190.654198.4
7.11-1004.80.04273340.619197.7

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MIR / Resolution: 3.3→100 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.89 / Occupancy max: 1 / Occupancy min: 1 / SU B: 27.171 / SU ML: 0.429 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.547 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2678 1611 2.5 %RANDOM
Rwork0.2329 ---
all0.2338 72065 --
obs0.2338 64758 89.86 %-
Solvent computationIon probe radii: 1.1 Å / Shrinkage radii: 1.1 Å / VDW probe radii: 1.3 Å / Solvent model: MASK
Displacement parametersBiso max: 236.75 Å2 / Biso mean: 70.769 Å2 / Biso min: 23.77 Å2
Baniso -1Baniso -2Baniso -3
1--0.97 Å20 Å20 Å2
2---2.25 Å20 Å2
3---3.22 Å2
Refinement stepCycle: LAST / Resolution: 3.3→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22128 0 66 0 22194
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01922716
X-RAY DIFFRACTIONr_angle_refined_deg1.261.94530796
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.56352742
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.54523.9521088
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.642153982
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.50615158
X-RAY DIFFRACTIONr_chiral_restr0.0940.23374
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02117152
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 THERMAL2.2599
1B223MEDIUM THERMAL2.8699
2B271MEDIUM POSITIONAL0.010.5
2B248TIGHT THERMAL4.7699
2B271MEDIUM THERMAL5.0599
3B121MEDIUM POSITIONAL0.020.5
3B132TIGHT THERMAL7.3599
3B121MEDIUM THERMAL7.8499
4B161MEDIUM POSITIONAL0.010.5
4B172TIGHT THERMAL11.399
4B161MEDIUM THERMAL10.9899
5B211MEDIUM POSITIONAL0.030.5
5B188TIGHT THERMAL19.3799
5B211MEDIUM THERMAL18.7699
6B204MEDIUM POSITIONAL0.020.5
6B204TIGHT THERMAL10.8599
6B204MEDIUM THERMAL10.8999
7B238MEDIUM POSITIONAL0.020.5
7B224TIGHT THERMAL3.999
7B238MEDIUM THERMAL3.999
8B363MEDIUM POSITIONAL0.020.5
8B320TIGHT THERMAL2.699
8B363MEDIUM THERMAL3.1199
9B258MEDIUM POSITIONAL0.020.5
9B256TIGHT THERMAL4.6399
9B258MEDIUM THERMAL4.8699
10B283MEDIUM POSITIONAL0.020.5
10B284TIGHT THERMAL6.0999
10B283MEDIUM THERMAL6.2599
11B73MEDIUM POSITIONAL0.030.5
11B80TIGHT THERMAL7.6799
11B73MEDIUM THERMAL7.8299
12B425MEDIUM POSITIONAL0.020.5
12B376TIGHT THERMAL19.3799
12B425MEDIUM THERMAL19.0599
13B293MEDIUM POSITIONAL0.040.5
13B300TIGHT THERMAL7.3499
13B293MEDIUM THERMAL7.6499
14B90MEDIUM POSITIONAL0.020.5
14B88TIGHT THERMAL3.9799
14B90MEDIUM THERMAL4.2199
15B108MEDIUM POSITIONAL0.020.5
15B116TIGHT THERMAL4.3899
15B108MEDIUM THERMAL4.6699
16B1055MEDIUM POSITIONAL0.030.5
16B1012TIGHT THERMAL3.2999
16B1055MEDIUM THERMAL3.4399
17D1186MEDIUM POSITIONAL0.020.5
17D1268TIGHT THERMAL10.6599
17D1186MEDIUM THERMAL10.9499
LS refinement shellResolution: 3.3→3.386 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 87 -
Rwork0.346 3639 -
all-3726 -
obs--73.38 %

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