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Yorodumi- PDB-6k9l: 4.27 Angstrom resolution cryo-EM structure of human dimeric ATM kinase -
+Open data
-Basic information
Entry | Database: PDB / ID: 6k9l | ||||||
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Title | 4.27 Angstrom resolution cryo-EM structure of human dimeric ATM kinase | ||||||
Components | Serine-protein kinase ATM | ||||||
Keywords | CELL CYCLE / DNA damage response / KInase | ||||||
Function / homology | Function and homology information DNA-dependent protein kinase activity / positive regulation of DNA catabolic process / histone H2AXS139 kinase activity / establishment of RNA localization to telomere / positive regulation of telomerase catalytic core complex assembly / positive regulation of DNA damage response, signal transduction by p53 class mediator / establishment of protein-containing complex localization to telomere / negative regulation of telomere capping / cellular response to nitrosative stress / Sensing of DNA Double Strand Breaks ...DNA-dependent protein kinase activity / positive regulation of DNA catabolic process / histone H2AXS139 kinase activity / establishment of RNA localization to telomere / positive regulation of telomerase catalytic core complex assembly / positive regulation of DNA damage response, signal transduction by p53 class mediator / establishment of protein-containing complex localization to telomere / negative regulation of telomere capping / cellular response to nitrosative stress / Sensing of DNA Double Strand Breaks / positive regulation of telomere maintenance via telomere lengthening / regulation of microglial cell activation / meiotic telomere clustering / pre-B cell allelic exclusion / male meiotic nuclear division / female meiotic nuclear division / histone mRNA catabolic process / pexophagy / cellular response to X-ray / regulation of telomere maintenance via telomerase / peptidyl-serine autophosphorylation / DNA double-strand break processing / lipoprotein catabolic process / V(D)J recombination / regulation of autophagosome assembly / oocyte development / Impaired BRCA2 binding to PALB2 / reciprocal meiotic recombination / DNA repair complex / Homologous DNA Pairing and Strand Exchange / 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 / 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 / TP53 Regulates Transcription of Caspase Activators and Caspases / mitotic spindle assembly checkpoint signaling / negative regulation of B cell proliferation / mitotic G2 DNA damage checkpoint signaling / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / Presynaptic phase of homologous DNA pairing and strand exchange / peroxisomal matrix / replicative senescence / Regulation of HSF1-mediated heat shock response / somitogenesis / signal transduction in response to DNA damage / cellular response to retinoic acid / ovarian follicle development / regulation of cellular response to heat / negative regulation of TORC1 signaling / positive regulation of telomere maintenance via telomerase / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / telomere maintenance / post-embryonic development / positive regulation of cell adhesion / Pexophagy / thymus development / determination of adult lifespan / regulation of signal transduction by p53 class mediator / DNA damage checkpoint signaling / regulation of autophagy / TP53 Regulates Transcription of DNA Repair Genes / Nonhomologous End-Joining (NHEJ) / Stabilization of p53 / Autodegradation of the E3 ubiquitin ligase COP1 / brain development / double-strand break repair via homologous recombination / G2/M DNA damage checkpoint / multicellular organism growth / DNA Damage/Telomere Stress Induced Senescence / HDR through Homologous Recombination (HRR) / Regulation of TP53 Activity through Methylation / cellular response to gamma radiation / Meiotic recombination / spindle / double-strand break repair via nonhomologous end joining / intrinsic apoptotic signaling pathway in response to DNA damage / cellular response to reactive oxygen species / positive regulation of neuron apoptotic process / cellular senescence / double-strand break repair / Regulation of TP53 Degradation / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / heart development / site of double-strand break / Processing of DNA double-strand break ends / cytoplasmic vesicle / peptidyl-serine phosphorylation / regulation of apoptotic process / neuron apoptotic process / Regulation of TP53 Activity through Phosphorylation / protein autophosphorylation / response to hypoxia / non-specific serine/threonine protein kinase / regulation of cell cycle / positive regulation of cell migration Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.27 Å | ||||||
Authors | Xiao, J. / Liu, M. / Qi, Y. / Chaban, Y. / Gao, C. / Tian, Y. / Yu, Z. / Li, J. / Zhang, P. / Xu, Y. | ||||||
Citation | Journal: Cell Res / Year: 2019 Title: Structural insights into the activation of ATM kinase. Authors: Jianxiong Xiao / Mengjie Liu / Yilun Qi / Yuriy Chaban / Chao Gao / Beiqing Pan / Yuan Tian / Zishuo Yu / Jie Li / Peijun Zhang / Yanhui Xu / | ||||||
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 | 6k9l.cif.gz | 801.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6k9l.ent.gz | 579.3 KB | Display | PDB format |
PDBx/mmJSON format | 6k9l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6k9l_validation.pdf.gz | 748.6 KB | Display | wwPDB validaton report |
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Full document | 6k9l_full_validation.pdf.gz | 774 KB | Display | |
Data in XML | 6k9l_validation.xml.gz | 105.3 KB | Display | |
Data in CIF | 6k9l_validation.cif.gz | 171.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k9/6k9l ftp://data.pdbj.org/pub/pdb/validation_reports/k9/6k9l | HTTPS FTP |
-Related structure data
Related structure data | 9950MC 9949C 9951C 6k9kC 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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1 |
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-Components
#1: Protein | Mass: 351127.688 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ATM / Cell line (production host): 293F / Production host: Homo sapiens (human) References: UniProt: Q13315, non-specific serine/threonine protein kinase |
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-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 human ATM (Ataxia telangiectasia mutated) kinase Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) / Cell: 293F |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 282 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company | ||||||||||||
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Microscopy | Model: FEI TITAN KRIOS | ||||||||||||
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER | ||||||||||||
Electron lens | Mode: BRIGHT FIELD | ||||||||||||
Image recording |
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-Processing
Software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.27 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 232416 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Refine LS restraints |
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