[English] 日本語
Yorodumi
- PDB-4jsv: mTOR kinase structure, mechanism and regulation. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4jsv
TitlemTOR kinase structure, mechanism and regulation.
Components
  • Serine/threonine-protein kinase mTOR
  • Target of rapamycin complex subunit LST8
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 / T-helper 1 cell lineage commitment / positive regulation of pentose-phosphate shunt / 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 / T-helper 1 cell lineage commitment / positive regulation of pentose-phosphate shunt / 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 / regulation of membrane permeability / heart valve morphogenesis / negative regulation of lysosome organization / RNA polymerase III type 3 promoter sequence-specific DNA binding / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / TORC1 complex / calcineurin-NFAT signaling cascade / nucleus localization / cellular response to methionine / voluntary musculoskeletal movement / regulation of osteoclast differentiation / TORC1 signaling / positive regulation of keratinocyte migration / cellular response to L-leucine / MTOR signalling / Amino acids regulate mTORC1 / cellular response to nutrient / regulation of autophagosome assembly / Energy dependent regulation of mTOR by LKB1-AMPK / energy reserve metabolic process / negative regulation of cell size / ruffle organization / cellular response to osmotic stress / negative regulation of protein localization to nucleus / anoikis / cardiac muscle cell development / positive regulation of transcription by RNA polymerase III / negative regulation of calcineurin-NFAT signaling cascade / regulation of myelination / negative regulation of macroautophagy / regulation of cell size / positive regulation of oligodendrocyte differentiation / Macroautophagy / positive regulation of actin filament polymerization / lysosome organization / positive regulation of myotube differentiation / oligodendrocyte differentiation / behavioral response to pain / Constitutive Signaling by AKT1 E17K in Cancer / germ cell development / mTORC1-mediated signalling / CD28 dependent PI3K/Akt signaling / : / HSF1-dependent transactivation / neuronal action potential / TOR signaling / positive regulation of TOR signaling / response to amino acid / endomembrane system / cellular response to nutrient levels / positive regulation of translational initiation / regulation of macroautophagy / 'de novo' pyrimidine nucleobase biosynthetic process / positive regulation of lamellipodium assembly / positive regulation of epithelial to mesenchymal transition / positive regulation of lipid biosynthetic process / heart morphogenesis / cardiac muscle contraction / regulation of cellular response to heat / phagocytic vesicle / positive regulation of stress fiber assembly / cytoskeleton organization / T cell costimulation / cellular response to starvation / positive regulation of glycolytic process / cellular response to amino acid starvation / protein serine/threonine kinase activator activity / phosphorylation / response to nutrient levels / negative regulation of autophagy / response to nutrient / VEGFR2 mediated vascular permeability / post-embryonic development / regulation of signal transduction by p53 class mediator / Regulation of PTEN gene transcription / positive regulation of translation / regulation of cell growth / macroautophagy / regulation of actin cytoskeleton organization / TP53 Regulates Metabolic Genes / phosphoprotein binding / cellular response to amino acid stimulus / protein destabilization / protein catabolic process / multicellular organism growth / regulation of circadian rhythm / PML body / cellular response to insulin stimulus / positive regulation of peptidyl-tyrosine phosphorylation / Regulation of TP53 Degradation
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 / : ...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 / : / 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. / 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. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / TRIFLUOROMAGNESATE / Serine/threonine-protein kinase mTOR / Target of rapamycin complex subunit LST8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3.5 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_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)342,23512
Polymers341,1214
Non-polymers1,1148
Water00
1
B: Serine/threonine-protein kinase mTOR
D: Target of rapamycin complex subunit LST8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,1176
Polymers170,5602
Non-polymers5574
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)171,1176
Polymers170,5602
Non-polymers5574
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

-
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 / 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-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-MGF / TRIFLUOROMAGNESATE


Mass: 81.300 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: F3Mg

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.46 Å3/Da / Density % sol: 64.5 %
Crystal growTemperature: 277 K / Method: hanging drop vapor diffusion / pH: 8.5
Details: PEG 8000, NaCl, pH 8.5, hanging drop vapor diffusion, temperature 277K

-
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: 3.5→100 Å / Num. all: 61200 / Num. obs: 57899 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.185 / Χ2: 0.865 / Net I/σ(I): 3.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.5-3.632.40.66550020.826183.6
3.63-3.772.60.58553850.899188.9
3.77-3.942.80.45858440.892196.8
3.94-4.153.10.35359490.865197.9
4.15-4.413.50.27958960.879197.5
4.41-4.753.50.19157650.858194.4
4.75-5.234.20.21960290.855198.7
5.23-5.984.50.27460190.94197.9
5.98-7.544.30.16258600.898194.8
7.54-1004.40.04861500.745195.2

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
DENZOdata reduction
SHARPphasing
RefinementMethod to determine structure: MIR / Resolution: 3.5→100 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.904 / Occupancy max: 1 / Occupancy min: 1 / SU B: 29.145 / SU ML: 0.433 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.63 / Stereochemistry target values: Engh & Huber / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2508 1294 2.6 %RANDOM
Rwork0.2309 ---
all0.2314 60586 --
obs0.2314 50681 83.65 %-
Solvent computationIon probe radii: 1.1 Å / Shrinkage radii: 1.1 Å / VDW probe radii: 1.3 Å / Solvent model: MASK
Displacement parametersBiso max: 274.9 Å2 / Biso mean: 74.4978 Å2 / Biso min: 28.19 Å2
Baniso -1Baniso -2Baniso -3
1--1.25 Å20 Å20 Å2
2---2.72 Å20 Å2
3---3.98 Å2
Refinement stepCycle: LAST / Resolution: 3.5→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22128 0 66 0 22194
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0222724
X-RAY DIFFRACTIONr_angle_refined_deg1.1561.94530794
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.05252742
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.23723.9521088
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.043153982
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.50715158
X-RAY DIFFRACTIONr_chiral_restr0.0830.23374
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 POSITIONAL0.010.05
1B80TIGHT POSITIONAL0.020.05
1B376TIGHT POSITIONAL0.010.05
1B300TIGHT POSITIONAL0.010.05
1B88TIGHT POSITIONAL0.010.05
1B116TIGHT POSITIONAL0.020.05
1B1012TIGHT POSITIONAL0.010.05
1B1268TIGHT POSITIONAL0.010.05
1B223MEDIUM POSITIONAL0.010.5
1B232TIGHT THERMAL2.4399
1B223MEDIUM THERMAL2.8299
2B271MEDIUM POSITIONAL0.010.5
2B248TIGHT THERMAL5.5599
2B271MEDIUM THERMAL5.6699
3B121MEDIUM POSITIONAL0.010.5
3B132TIGHT THERMAL6.3799
3B121MEDIUM THERMAL7.1999
4B161MEDIUM POSITIONAL0.010.5
4B172TIGHT THERMAL11.0399
4B161MEDIUM THERMAL11.5699
5B211MEDIUM POSITIONAL0.020.5
5B188TIGHT THERMAL22.4999
5B211MEDIUM THERMAL20.6999
6B204MEDIUM POSITIONAL0.020.5
6B204TIGHT THERMAL10.2599
6B204MEDIUM THERMAL10.3299
7B238MEDIUM POSITIONAL0.020.5
7B224TIGHT THERMAL3.0499
7B238MEDIUM THERMAL2.7899
8B363MEDIUM POSITIONAL0.020.5
8B320TIGHT THERMAL2.7799
8B363MEDIUM THERMAL3.1399
9B258MEDIUM POSITIONAL0.020.5
9B256TIGHT THERMAL4.4599
9B258MEDIUM THERMAL4.8299
10B283MEDIUM POSITIONAL0.020.5
10B284TIGHT THERMAL6.7999
10B283MEDIUM THERMAL6.9499
11B73MEDIUM POSITIONAL0.020.5
11B80TIGHT THERMAL9.1999
11B73MEDIUM THERMAL9.4699
12B425MEDIUM POSITIONAL0.010.5
12B376TIGHT THERMAL18.5299
12B425MEDIUM THERMAL18.0399
13B293MEDIUM POSITIONAL0.020.5
13B300TIGHT THERMAL8.4699
13B293MEDIUM THERMAL8.599
14B90MEDIUM POSITIONAL0.020.5
14B88TIGHT THERMAL4.0499
14B90MEDIUM THERMAL4.8299
15B108MEDIUM POSITIONAL0.010.5
15B116TIGHT THERMAL5.6399
15B108MEDIUM THERMAL5.8199
16B1055MEDIUM POSITIONAL0.020.5
16B1012TIGHT THERMAL4.5799
16B1055MEDIUM THERMAL4.7899
17D1186MEDIUM POSITIONAL0.020.5
17D1268TIGHT THERMAL10.7199
17D1186MEDIUM THERMAL11.1299
LS refinement shellResolution: 3.5→3.591 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 59 -
Rwork0.346 2773 -
all-2832 -
obs--65.66 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlc1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more