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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 / transferase
Function / homologyFKBP12-rapamycin binding domain / FATC domain / Macroautophagy / Armadillo-type fold / PIP3 activates AKT signaling / PIK-related kinase / Tetratricopeptide-like helical domain superfamily / Armadillo-like helical / Quinoprotein alcohol dehydrogenase-like superfamily / Protein kinase-like domain superfamily ...FKBP12-rapamycin binding domain / FATC domain / Macroautophagy / Armadillo-type fold / PIP3 activates AKT signaling / PIK-related kinase / Tetratricopeptide-like helical domain superfamily / Armadillo-like helical / Quinoprotein alcohol dehydrogenase-like superfamily / Protein kinase-like domain superfamily / FKBP12-rapamycin binding domain / PIK-related kinase, FAT / WD40-repeat-containing domain / WD40 repeat / Phosphatidylinositol 3-/4-kinase, catalytic domain / FATC domain profile. / FAT domain profile. / Trp-Asp (WD) repeats signature. / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3- and 4-kinases signature 2. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / Phosphatidylinositol 3- and 4-kinases family profile. / mTOR signalling / WD40/YVTN repeat-like-containing domain superfamily / Phosphatidylinositol 3/4-kinase, conserved site / Constitutive Signaling by AKT1 E17K in Cancer / FATC domain / FAT domain / Phosphatidylinositol 3- and 4-kinase / Regulation of PTEN gene transcription / WD40 repeat, conserved site / WD domain, G-beta repeat / Target of rapamycin complex subunit LST8 / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Regulation of TP53 Degradation / Domain of unknown function (DUF3385) / TP53 Regulates Metabolic Genes / VEGFR2 mediated vascular permeability / G-protein beta WD-40 repeat / mTORC1-mediated signalling / HSF1-dependent transactivation / Domain of unknown function DUF3385, target of rapamycin protein / FKBP12-rapamycin binding domain superfamily / Serine/threonine-protein kinase TOR / Energy dependent regulation of mTOR by LKB1-AMPK / CD28 dependent PI3K/Akt signaling / regulation of fatty acid beta-oxidation / negative regulation of iodide transmembrane transport / positive regulation of skeletal muscle hypertrophy / positive regulation of granulosa cell proliferation / negative regulation of cholangiocyte apoptotic process / positive regulation of cholangiocyte proliferation / positive regulation of cytoplasmic translational initiation / positive regulation of wound healing, spreading of epidermal cells / RNA polymerase III type 2 promoter DNA binding / negative regulation of muscle atrophy / RNA polymerase III type 1 promoter DNA binding / positive regulation of eating behavior / RNA polymerase III type 3 promoter DNA binding / cellular response to leucine starvation / cardiac muscle cell development / regulation of carbohydrate utilization / regulation of response to food / TFIIIC-class transcription factor binding / cellular response to leucine / TORC1 complex / heart valve morphogenesis / TORC1 signaling / TORC2 complex / positive regulation of sensory perception of pain / regulation of membrane permeability / positive regulation of keratinocyte migration / positive regulation of glial cell proliferation / regulation of brown fat cell differentiation / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / voluntary musculoskeletal movement / regulation of glycogen biosynthetic process / positive regulation of neuron maturation / energy reserve metabolic process / regulation of osteoclast differentiation / mRNA stabilization / cellular response to nutrient levels / ruffle organization / positive regulation of TOR signaling / negative regulation of cell size / anoikis / positive regulation of transcription by RNA polymerase III / regulation of myelination / phosphatidylinositol 3-kinase complex / positive regulation of cell growth involved in cardiac muscle cell development / regulation of cell size / positive regulation of dendritic spine development / positive regulation of lamellipodium assembly / negative regulation of macroautophagy / spinal cord development / TOR signaling / social behavior / negative regulation of calcineurin-NFAT signaling cascade / response to morphine
Function and homology information
Specimen sourceHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / 3.3 Å resolution
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 22, 2013 / Release: May 1, 2013
RevisionDateData content typeGroupProviderType
1.0May 1, 2013Structure modelrepositoryInitial release
1.1May 8, 2013Structure modelStructure summary
1.2May 29, 2013Structure modelDatabase references

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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
Polyers341,1214
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
Polyers170,5602
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
Polyers170,5602
Non-polymers5723
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
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-MP 2 21 21

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Components

#1: Protein/peptide Serine/threonine-protein kinase mTOR / 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: (gene. exp.) Homo sapiens (human) / Gene: FRAP, FRAP1, FRAP2, MTOR, RAFT1, RAPT1 / Plasmid name: pcDNA3.1(+)hygromycin / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human)
References: UniProt: P42345, non-specific serine/threonine protein kinase
#2: Protein/peptide Target of rapamycin complex subunit LST8 / MTOR / 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: (gene. exp.) Homo sapiens (human) / Gene: GBL, LST8, MLST8 / Plasmid name: 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 / 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 / Formula: Mg / Magnesium

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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 / Density percent sol: 64.5 %
Crystal growTemp: 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 kelvins
SourceSource: SYNCHROTRON / Type: APS BEAMLINE 24-ID-C / Synchrotron site: APS / Beamline: 24-ID-C / Wavelength: 0.97925
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Collection date: Dec 10, 2011
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97925 Å / Relative weight: 1
ReflectionD resolution high: 3.3 Å / D resolution low: 1 Å / Number obs: 70381 / Rmerge I obs: 0.149 / Chi squared: 0.729 / NetI over sigmaI: 4.1 / Redundancy: 4.4 % / Percent possible obs: 98.5
Reflection shell

Diffraction ID: 1

Rmerge I obsHighest resolutionLowest resolutionNumber unique allChi squaredRedundancyPercent possible all
0.6123.3003.42067170.8222.50095.200
0.4513.4203.55068050.8623.20096.400
0.4333.5503.72070250.8804.40099.400
0.3263.7203.91070270.8654.60099.500
0.2203.9104.16070540.7314.80099.700
0.1444.1604.48070970.6814.70099.600
0.1094.4804.93070230.6614.90098.900
0.1164.9305.64071800.6615.10099.900
0.0975.6407.11071190.6544.70098.400
0.0427.110100.00073340.6194.80097.700

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Processing

Software
NameVersionClassificationContact authorContact author emailLocationTypeLanguageDate
SCALEPACKdata scalingZbyszek Otwinowskihkl[at]hkl-xray.comhttp://www.hkl-xray.com/program
REFMAC5.6.0117refinementGarib N. Murshudovgarib[at]ysbl.york.ac.ukhttp://www.ccp4.ac.uk/dist/html/refmac5.htmlprogramFortran_77
PDB_EXTRACT3.11data extractionPDBdeposit[at]deposit.rcsb.orghttp://sw-tools.pdb.org/apps/PDB_EXTRACT/packageC++April 22, 2011
RefineMethod to determine structure: MIR / Correlation coeff Fo to Fc: 0.914 / Correlation coeff Fo to Fc free: 0.89 / Details: U VALUES : REFINED INDIVIDUALLY / Occupancy max: 1 / Occupancy min: 1 / Overall SU B: 27.171 / Overall SU ML: 0.429 / R Free selection details: RANDOM / Cross valid method: THROUGHOUT / Sigma F: 0 / Overall ESU R Free: 0.547 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Solvent computationSolvent ion probe radii: 1.1 Å / Solvent shrinkage radii: 1.1 Å / Solvent vdw probe radii: 1.3 Å / Solvent model details: MASK
Displacement parametersB iso max: 236.75 Å2 / B iso mean: 70.769 Å2 / B iso min: 23.77 Å2 / Aniso B11: -0.97 Å2 / Aniso B12: 0 Å2 / Aniso B13: 0 Å2 / Aniso B22: -2.25 Å2 / Aniso B23: 0 Å2 / Aniso B33: 3.22 Å2
Least-squares processR factor R free: 0.2678 / R factor R work: 0.2329 / R factor all: 0.2338 / R factor obs: 0.2338 / Highest resolution: 3.3 Å / Lowest resolution: 1 Å / Number reflection R free: 1611 / Number reflection all: 72065 / Number reflection obs: 64758 / Percent reflection R free: 2.5 / Percent reflection obs: 89.86
Refine hist #LASTHighest resolution: 3.3 Å / Lowest resolution: 1 Å
Number of atoms included #LASTProtein: 22128 / Nucleic acid: 0 / Ligand: 66 / Solvent: 0 / Total: 22194
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01922716
X-RAY DIFFRACTIONr_angle_refined_deg1.2601.94530796
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5635.0002742
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.54523.9521088
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.64215.0003982
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.50615.000158
X-RAY DIFFRACTIONr_chiral_restr0.0940.2003374
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02117152
Refine LS restraints ncs

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

Auth asym IDEns IDNumberTypeRms dev positionWeight position
B1284TIGHT POSITIONAL0.0200.050
B180TIGHT POSITIONAL0.0200.050
B1376TIGHT POSITIONAL0.0100.050
B1300TIGHT POSITIONAL0.0200.050
B188TIGHT POSITIONAL0.0200.050
B1116TIGHT POSITIONAL0.0200.050
B11012TIGHT POSITIONAL0.0200.050
B11268TIGHT POSITIONAL0.0200.050
B1223MEDIUM POSITIONAL0.0200.500
B1232TIGHT THERMAL2.25099.000
B1223MEDIUM THERMAL2.86099.000
B2271MEDIUM POSITIONAL0.0100.500
B2248TIGHT THERMAL4.76099.000
B2271MEDIUM THERMAL5.05099.000
B3121MEDIUM POSITIONAL0.0200.500
B3132TIGHT THERMAL7.35099.000
B3121MEDIUM THERMAL7.84099.000
B4161MEDIUM POSITIONAL0.0100.500
B4172TIGHT THERMAL11.30099.000
B4161MEDIUM THERMAL10.98099.000
B5211MEDIUM POSITIONAL0.0300.500
B5188TIGHT THERMAL19.37099.000
B5211MEDIUM THERMAL18.76099.000
B6204MEDIUM POSITIONAL0.0200.500
B6204TIGHT THERMAL10.85099.000
B6204MEDIUM THERMAL10.89099.000
B7238MEDIUM POSITIONAL0.0200.500
B7224TIGHT THERMAL3.90099.000
B7238MEDIUM THERMAL3.90099.000
B8363MEDIUM POSITIONAL0.0200.500
B8320TIGHT THERMAL2.60099.000
B8363MEDIUM THERMAL3.11099.000
B9258MEDIUM POSITIONAL0.0200.500
B9256TIGHT THERMAL4.63099.000
B9258MEDIUM THERMAL4.86099.000
B10283MEDIUM POSITIONAL0.0200.500
B10284TIGHT THERMAL6.09099.000
B10283MEDIUM THERMAL6.25099.000
B1173MEDIUM POSITIONAL0.0300.500
B1180TIGHT THERMAL7.67099.000
B1173MEDIUM THERMAL7.82099.000
B12425MEDIUM POSITIONAL0.0200.500
B12376TIGHT THERMAL19.37099.000
B12425MEDIUM THERMAL19.05099.000
B13293MEDIUM POSITIONAL0.0400.500
B13300TIGHT THERMAL7.34099.000
B13293MEDIUM THERMAL7.64099.000
B1490MEDIUM POSITIONAL0.0200.500
B1488TIGHT THERMAL3.97099.000
B1490MEDIUM THERMAL4.21099.000
B15108MEDIUM POSITIONAL0.0200.500
B15116TIGHT THERMAL4.38099.000
B15108MEDIUM THERMAL4.66099.000
B161055MEDIUM POSITIONAL0.0300.500
B161012TIGHT THERMAL3.29099.000
B161055MEDIUM THERMAL3.43099.000
D171186MEDIUM POSITIONAL0.0200.500
D171268TIGHT THERMAL10.65099.000
D171186MEDIUM THERMAL10.94099.000
Refine LS shellHighest resolution: 3.3 Å / R factor R free: 0.353 / R factor R work: 0.346 / Lowest resolution: 3.386 Å / Number reflection R free: 87 / Number reflection R work: 3639 / Number reflection all: 3726 / Total number of bins used: 20 / Percent reflection obs: 73.38

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