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Yorodumi- PDB-6hka: The solution structure of the micelle-associated FATC domain of t... -
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-Basic information
Entry | Database: PDB / ID: 6hka | ||||||
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Title | The solution structure of the micelle-associated FATC domain of the human protein kinase ataxia telangiectasia mutated (ATM) | ||||||
Components | Immunoglobulin G-binding protein G,Serine-protein kinase ATM | ||||||
Keywords | TRANSFERASE / Ataxia telangiectasia mutated (ATM) / FATC domain / phosphatidylinositol-3-kinase-related kinase (PIKKs) / ser/thr kinase / membrane binding | ||||||
Function / homology | Function and homology information positive regulation of DNA catabolic process / establishment of RNA localization to telomere / positive regulation of telomerase catalytic core complex assembly / cellular response to nitrosative stress / negative regulation of telomere capping / positive regulation of DNA damage response, signal transduction by p53 class mediator / establishment of protein-containing complex localization to telomere / regulation of microglial cell activation / Sensing of DNA Double Strand Breaks / positive regulation of telomere maintenance via telomere lengthening ...positive regulation of DNA catabolic process / establishment of RNA localization to telomere / positive regulation of telomerase catalytic core complex assembly / cellular response to nitrosative stress / negative regulation of telomere capping / positive regulation of DNA damage response, signal transduction by p53 class mediator / establishment of protein-containing complex localization to telomere / regulation of microglial cell activation / Sensing of DNA Double Strand Breaks / positive regulation of telomere maintenance via telomere lengthening / meiotic telomere clustering / lipoprotein catabolic process / pre-B cell allelic exclusion / DNA-dependent protein kinase activity / histone H2AXS139 kinase activity / male meiotic nuclear division / histone mRNA catabolic process / female meiotic nuclear division / regulation of telomere maintenance via telomerase / pexophagy / cellular response to X-ray / peptidyl-serine autophosphorylation / V(D)J recombination / oocyte development / Impaired BRCA2 binding to PALB2 / reciprocal meiotic recombination / DNA repair complex / IgG binding / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Homologous DNA Pairing and Strand Exchange / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Resolution of D-loop Structures through Holliday Junction Intermediates / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / 1-phosphatidylinositol-3-kinase activity / response to ionizing radiation / mitotic spindle assembly checkpoint signaling / TP53 Regulates Transcription of Caspase Activators and Caspases / negative regulation of B cell proliferation / mitotic G2 DNA damage checkpoint signaling / Presynaptic phase of homologous DNA pairing and strand exchange / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / peroxisomal matrix / positive regulation of cell adhesion / replicative senescence / Regulation of HSF1-mediated heat shock response / somitogenesis / regulation of cellular response to heat / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / signal transduction in response to DNA damage / cellular response to retinoic acid / ovarian follicle development / negative regulation of TORC1 signaling / positive regulation of telomere maintenance via telomerase / Pexophagy / telomere maintenance / post-embryonic development / thymus development / DNA damage checkpoint signaling / regulation of signal transduction by p53 class mediator / regulation of autophagy / determination of adult lifespan / TP53 Regulates Transcription of DNA Repair Genes / Nonhomologous End-Joining (NHEJ) / Stabilization of p53 / double-strand break repair via homologous recombination / Autodegradation of the E3 ubiquitin ligase COP1 / brain development / multicellular organism growth / cellular response to gamma radiation / HDR through Homologous Recombination (HRR) / G2/M DNA damage checkpoint / Regulation of TP53 Activity through Methylation / DNA Damage/Telomere Stress Induced Senescence / spindle / Meiotic recombination / cellular response to reactive oxygen species / double-strand break repair via nonhomologous end joining / positive regulation of neuron apoptotic process / intrinsic apoptotic signaling pathway in response to DNA damage / double-strand break repair / cellular senescence / Regulation of TP53 Degradation / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / heart development / Processing of DNA double-strand break ends / cytoplasmic vesicle / peptidyl-serine phosphorylation / neuron apoptotic process / regulation of apoptotic process / Regulation of TP53 Activity through Phosphorylation / protein autophosphorylation / response to hypoxia / regulation of cell cycle / non-specific serine/threonine protein kinase / positive regulation of cell migration / positive regulation of apoptotic process / protein phosphorylation Similarity search - Function | ||||||
Biological species | Streptococcus sp. group G (bacteria) Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Abd Rahim, M.S. / Dames, S.A. | ||||||
Funding support | Germany, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2019 Title: NMR- and MD simulation-based structural characterization of the membrane-associating FATC domain of ataxia telangiectasia mutated. Authors: Abd Rahim, M.S. / Cherniavskyi, Y.K. / Tieleman, D.P. / Dames, S.A. #1: Journal: Biomol NMR Assign. / Year: 2018 Title: 1H, 15N and 13C chemical shift assignments of the micelle immersed FAT C-terminal (FATC) domains of the human protein kinases ataxia-telangiectasia mutated (ATM) and DNA-dependent protein ...Title: 1H, 15N and 13C chemical shift assignments of the micelle immersed FAT C-terminal (FATC) domains of the human protein kinases ataxia-telangiectasia mutated (ATM) and DNA-dependent protein kinase catalytic subunit (DNA-PKcs)fused to the B1 domain of streptococcal protein G (GB1) Authors: Abd Rahim, M.S. / Sommer, L.A.M. / Wacker, A. / Schaad, M. / Dames, S.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hka.cif.gz | 222.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hka.ent.gz | 183.3 KB | Display | PDB format |
PDBx/mmJSON format | 6hka.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hk/6hka ftp://data.pdbj.org/pub/pdb/validation_reports/hk/6hka | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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NMR ensembles |
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-Components
#1: Antibody | Mass: 11021.240 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: N-terminally GB1-tagged (1-56), linker: thrombin and enterokinase sites (57-67), FATC domain of ATM (68-100),N-terminally GB1-tagged (1-56), linker: thrombin and enterokinase sites (57-67), ...Details: N-terminally GB1-tagged (1-56), linker: thrombin and enterokinase sites (57-67), FATC domain of ATM (68-100),N-terminally GB1-tagged (1-56), linker: thrombin and enterokinase sites (57-67), FATC domain of ATM (68-100) Source: (gene. exp.) Streptococcus sp. group G (bacteria), (gene. exp.) Homo sapiens (human) Gene: spg, ATM / Plasmid: pGEV2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: P19909, UniProt: Q13315, non-specific serine/threonine protein kinase |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | Details: 50 mM Tris, 100 mM NaCl, 150 mM DPC (usually deuterated d38-DPC) Ionic strength: 100 mM / Label: condition_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 4 | |||||||||||||||
NMR representative | Selection criteria: lowest energy | |||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 20 |