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Yorodumi- PDB-3jbz: Crystal structure of mTOR docked into EM map of dimeric ATM kinase -
+Open data
-Basic information
Entry | Database: PDB / ID: 3jbz | ||||||
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Title | Crystal structure of mTOR docked into EM map of dimeric ATM kinase | ||||||
Components | Serine/threonine-protein kinase mTOR | ||||||
Keywords | TRANSFERASE / mTOR / PIKK | ||||||
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 / T-helper 1 cell lineage commitment / regulation of locomotor rhythm / positive regulation of pentose-phosphate shunt / positive regulation of wound healing, spreading of epidermal cells / cellular response to leucine starvation / TORC2 complex / TFIIIC-class transcription factor complex binding ...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 / T-helper 1 cell lineage commitment / regulation of locomotor rhythm / positive regulation of pentose-phosphate shunt / positive regulation of wound healing, spreading of epidermal cells / cellular response to leucine starvation / TORC2 complex / TFIIIC-class transcription factor complex binding / regulation of membrane permeability / negative regulation of lysosome organization / heart valve morphogenesis / nucleus localization / 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 / cellular response to methionine / TORC1 signaling / regulation of osteoclast differentiation / voluntary musculoskeletal movement / positive regulation of keratinocyte migration / cellular response to L-leucine / Amino acids regulate mTORC1 / MTOR signalling / 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 / regulation of cell size / negative regulation of macroautophagy / positive regulation of oligodendrocyte differentiation / positive regulation of actin filament polymerization / lysosome organization / Macroautophagy / positive regulation of myotube differentiation / behavioral response to pain / oligodendrocyte differentiation / 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 / response to amino acid / regulation of macroautophagy / cellular response to nutrient levels / positive regulation of translational initiation / endomembrane system / 'de novo' pyrimidine nucleobase biosynthetic process / positive regulation of lamellipodium assembly / phagocytic vesicle / heart morphogenesis / positive regulation of lipid biosynthetic process / positive regulation of epithelial to mesenchymal transition / cardiac muscle contraction / regulation of cellular response to heat / cytoskeleton organization / positive regulation of stress fiber assembly / phosphorylation / T cell costimulation / positive regulation of glycolytic process / cellular response to amino acid starvation / negative regulation of autophagy / cellular response to starvation / response to nutrient levels / response to nutrient / post-embryonic development / VEGFR2 mediated vascular permeability / regulation of signal transduction by p53 class mediator / Regulation of PTEN gene transcription / positive regulation of translation / regulation of cell growth / regulation of actin cytoskeleton organization / TP53 Regulates Metabolic Genes / macroautophagy / 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 / rhythmic process / PIP3 activates AKT signaling Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / negative staining / Resolution: 28 Å | ||||||
Authors | Lau, W.C.Y. | ||||||
Citation | Journal: Cell Cycle / Year: 2016 Title: Structure of the human dimeric ATM kinase. Authors: Wilson C Y Lau / Yinyin Li / Zhe Liu / Yuanzhu Gao / Qinfen Zhang / Michael S Y Huen / Abstract: DNA-double strand breaks activate the serine/threonine protein kinase ataxia-telangiectasia mutated (ATM) to initiate DNA damage signal transduction. This activation process involves ...DNA-double strand breaks activate the serine/threonine protein kinase ataxia-telangiectasia mutated (ATM) to initiate DNA damage signal transduction. This activation process involves autophosphorylation and dissociation of inert ATM dimers into monomers that are catalytically active. Using single-particle electron microscopy (EM), we determined the structure of dimeric ATM in its resting state. The EM map could accommodate the crystal structure of the N-terminal truncated mammalian target of rapamycin (mTOR), a closely related enzyme of the phosphatidylinositol 3-kinase-related protein kinase (PIKK) family, allowing for the localization of the N- and the C-terminal regions of ATM. In the dimeric structure, the actives sites are buried, restricting the access of the substrates to these sites. The unanticipated domain organization of ATM provides a basis for understanding its mechanism of inhibition. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 3jbz.cif.gz | 212.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3jbz.ent.gz | 160.8 KB | Display | PDB format |
PDBx/mmJSON format | 3jbz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3jbz_validation.pdf.gz | 766.4 KB | Display | wwPDB validaton report |
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Full document | 3jbz_full_validation.pdf.gz | 787.8 KB | Display | |
Data in XML | 3jbz_validation.xml.gz | 31.2 KB | Display | |
Data in CIF | 3jbz_validation.cif.gz | 47.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jb/3jbz ftp://data.pdbj.org/pub/pdb/validation_reports/jb/3jbz | HTTPS FTP |
-Related structure data
Related structure data | 6501MC 6499C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 133753.281 Da / Num. of mol.: 1 Fragment: C-terminal domain (UNP RESIDUES 1385-2020, 2119-2549) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FRAP, FRAP1, FRAP2, MTOR, RAFT1, RAPT1 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) References: UniProt: P42345, non-specific serine/threonine protein kinase | ||
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#2: Chemical | ChemComp-ADP / | ||
#3: Chemical | #4: Chemical | ChemComp-MGF / | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: dimeric ATM kinase / Type: COMPLEX |
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Molecular weight | Value: 0.7 MDa / Experimental value: NO |
Buffer solution | Name: 25 mM Tris pH 8.0, 100 mM NaCl, 1 mM TCEP, 10% glycerol pH: 8 / Details: 25 mM Tris, 100 mM NaCl, 1 mM TCEP, 10% glycerol |
Specimen | Conc.: 0.02 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: NO |
EM staining | Type: NEGATIVE / Details: 2% uranyl acetate / Material: uranyl acetate |
Specimen support | Details: continuous carbon grid |
-Electron microscopy imaging
Microscopy | Model: JEOL 2010 / Date: Sep 1, 2015 |
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Electron gun | Electron source: LAB6 / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 50000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 1000 nm / Cs: 2 mm |
Specimen holder | Temperature: 293 K |
Image recording | Electron dose: 25 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Num. of real images: 251 |
Image scans | Num. digital images: 251 |
-Processing
EM software |
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Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||
3D reconstruction | Resolution: 28 Å / Resolution method: FSC 0.143 CUT-OFF / Symmetry type: POINT | ||||||||||||
Atomic model building | PDB-ID: 4JSV Accession code: 4JSV / Source name: PDB / Type: experimental model | ||||||||||||
Refinement step | Cycle: LAST
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