Reviews - 5luq mentioned but not cited (3)
- Nonhomologous DNA end-joining for repair of DNA double-strand breaks. Pannunzio NR, Watanabe G, Lieber MR. J. Biol. Chem. 293 10512-10523 (2018)
- Druggable binding sites in the multicomponent assemblies that characterise DNA double-strand-break repair through non-homologous end joining. Kefala Stavridi A, Appleby R, Liang S, Blundell TL, Chaplin AK. Essays Biochem 64 791-806 (2020)
- Structural Insights into TOR Signaling. Tafur L, Kefauver J, Loewith R. Genes (Basel) 11 (2020)
Articles - 5luq mentioned but not cited (17)
- Structural basis of long-range to short-range synaptic transition in NHEJ. Chen S, Lee L, Naila T, Fishbain S, Wang A, Tomkinson AE, Lees-Miller SP, He Y. Nature 593 294-298 (2021)
- Structure of an activated DNA-PK and its implications for NHEJ. Chen X, Xu X, Chen Y, Cheung JC, Wang H, Jiang J, de Val N, Fox T, Gellert M, Yang W. Mol Cell 81 801-810.e3 (2021)
- Uncovering DNA-PKcs ancient phylogeny, unique sequence motifs and insights for human disease. Lees-Miller JP, Cobban A, Katsonis P, Bacolla A, Tsutakawa SE, Hammel M, Meek K, Anderson DW, Lichtarge O, Tainer JA, Lees-Miller SP. Prog Biophys Mol Biol 163 87-108 (2021)
- Visualizing functional dynamicity in the DNA-dependent protein kinase holoenzyme DNA-PK complex by integrating SAXS with cryo-EM. Hammel M, Rosenberg DJ, Bierma J, Hura GL, Thapar R, Lees-Miller SP, Tainer JA. Prog Biophys Mol Biol 163 74-86 (2021)
- Cryo-EM structure of the DNA-PK holoenzyme. Sharif H, Li Y, Dong Y, Dong L, Wang WL, Mao Y, Wu H. Proc. Natl. Acad. Sci. U.S.A. 114 7367-7372 (2017)
- The active DNA-PK holoenzyme occupies a tensed state in a staggered synaptic complex. Hepburn M, Saltzberg DJ, Lee L, Fang S, Atkinson C, Strynadka NCJ, Sali A, Lees-Miller SP, Schriemer DC. Structure 29 467-478.e6 (2021)
- Cryo-EM structure of the SAGA and NuA4 coactivator subunit Tra1 at 3.7 angstrom resolution. Díaz-Santín LM, Lukoyanova N, Aciyan E, Cheung AC. Elife 6 (2017)
- Cryo-EM structure of human DNA-PK holoenzyme. Yin X, Liu M, Tian Y, Wang J, Xu Y. Cell Res. 27 1341-1350 (2017)
- Architecture of the Saccharomyces cerevisiae NuA4/TIP60 complex. Wang X, Ahmad S, Zhang Z, Côté J, Cai G. Nat Commun 9 1147 (2018)
- Stages, scaffolds and strings in the spatial organisation of non-homologous end joining: Insights from X-ray diffraction and Cryo-EM. Liang S, Chaplin AK, Stavridi AK, Appleby R, Hnizda A, Blundell TL. Prog Biophys Mol Biol 163 60-73 (2021)
- DNA-PKcs, Allostery, and DNA Double-Strand Break Repair: Defining the Structure and Setting the Stage. Chirgadze DY, Ascher DB, Blundell TL, Sibanda BL. Meth. Enzymol. 592 145-157 (2017)
- Structural analysis of the basal state of the Artemis:DNA-PKcs complex. Watanabe G, Lieber MR, Williams DR. Nucleic Acids Res 50 7697-7720 (2022)
- Structural step forward for NHEJ. Watanabe G, Lieber MR, Williams D. Cell Res. 27 1304-1306 (2017)
- Cryo-EM Structure of Nucleotide-Bound Tel1ATM Unravels the Molecular Basis of Inhibition and Structural Rationale for Disease-Associated Mutations. Yates LA, Williams RM, Hailemariam S, Ayala R, Burgers P, Zhang X. Structure 28 96-104.e3 (2020)
- Human Genetic Markers and Structural Prediction of Plasmodium falciparum Multidrug Resistance Gene (pfmdr1) for Ligand Binding in Pregnant Women Attending General Hospital Minna. Lawal B, Shittu OK, Abubakar A, Kabiru AY. J Environ Public Health 2018 3984316 (2018)
- SSEThread: Integrative threading of the DNA-PKcs sequence based on data from chemical cross-linking and hydrogen deuterium exchange. Saltzberg DJ, Hepburn M, Pilla KB, Schriemer DC, Lees-Miller SP, Blundell TL, Sali A. Prog. Biophys. Mol. Biol. 147 92-102 (2019)
- TBC1D15 deficiency protects against doxorubicin cardiotoxicity via inhibiting DNA-PKcs cytosolic retention and DNA damage. Yu W, Xu H, Sun Z, Du Y, Sun S, Abudureyimu M, Zhang M, Tao J, Ge J, Ren J, Zhang Y. Acta Pharm Sin B 13 4823-4839 (2023)
Reviews citing this publication (31)
- ATM, ATR, and DNA-PK: The Trinity at the Heart of the DNA Damage Response. Blackford AN, Jackson SP. Mol. Cell 66 801-817 (2017)
- Non-homologous DNA end joining and alternative pathways to double-strand break repair. Chang HHY, Pannunzio NR, Adachi N, Lieber MR. Nat. Rev. Mol. Cell Biol. 18 495-506 (2017)
- ATM, ATR and DNA-PKcs kinases-the lessons from the mouse models: inhibition ≠ deletion. Menolfi D, Zha S. Cell Biosci 10 8 (2020)
- DNA-PKcs: A Targetable Protumorigenic Protein Kinase. Dylgjeri E, Knudsen KE. Cancer Res 82 523-533 (2022)
- Structural basis of homologous recombination. Sun Y, McCorvie TJ, Yates LA, Zhang X. Cell Mol Life Sci 77 3-18 (2020)
- X-ray scattering reveals disordered linkers and dynamic interfaces in complexes and mechanisms for DNA double-strand break repair impacting cell and cancer biology. Hammel M, Tainer JA. Protein Sci 30 1735-1756 (2021)
- Combating mutations in genetic disease and drug resistance: understanding molecular mechanisms to guide drug design. Albanaz ATS, Rodrigues CHM, Pires DEV, Ascher DB. Expert Opin Drug Discov 12 553-563 (2017)
- The MRE11-RAD50-NBS1 Complex Conducts the Orchestration of Damage Signaling and Outcomes to Stress in DNA Replication and Repair. Syed A, Tainer JA. Annu. Rev. Biochem. 87 263-294 (2018)
- Repair of DNA Double-Strand Breaks by the Nonhomologous End Joining Pathway. Stinson BM, Loparo JJ. Annu Rev Biochem 90 137-164 (2021)
- What Combined Measurements From Structures and Imaging Tell Us About DNA Damage Responses. Brosey CA, Ahmed Z, Lees-Miller SP, Tainer JA. Meth. Enzymol. 592 417-455 (2017)
- Phosphoproteomics Meets Chemical Genetics: Approaches for Global Mapping and Deciphering the Phosphoproteome. Jurcik J, Sivakova B, Cipakova I, Selicky T, Stupenova E, Jurcik M, Osadska M, Barath P, Cipak L. Int J Mol Sci 21 E7637 (2020)
- Role of PRKDC in cancer initiation, progression, and treatment. Chen Y, Li Y, Xiong J, Lan B, Wang X, Liu J, Lin J, Fei Z, Zheng X, Chen C. Cancer Cell Int 21 563 (2021)
- The Ku complex: recent advances and emerging roles outside of non-homologous end-joining. Abbasi S, Parmar G, Kelly RD, Balasuriya N, Schild-Poulter C. Cell Mol Life Sci 78 4589-4613 (2021)
- The Multifaceted Roles of Ku70/80. Zahid S, Seif El Dahan M, Iehl F, Fernandez-Varela P, Le Du MH, Ropars V, Charbonnier JB. Int J Mol Sci 22 4134 (2021)
- The role of DNA-PK in aging and energy metabolism. Chung JH. FEBS J. 285 1959-1972 (2018)
- Branching the Tel2 pathway for exact fit on phosphatidylinositol 3-kinase-related kinases. Sugimoto K. Curr. Genet. 64 965-970 (2018)
- The Role of Hsp90-R2TP in Macromolecular Complex Assembly and Stabilization. Lynham J, Houry WA. Biomolecules 12 1045 (2022)
- Autophosphorylation and Self-Activation of DNA-Dependent Protein Kinase. Kurosawa A. Genes (Basel) 12 1091 (2021)
- DNA Repair in Haploid Context. Mourrain L, Boissonneault G. Int J Mol Sci 22 12418 (2021)
- DNA-PK as an Emerging Therapeutic Target in Cancer. Mohiuddin IS, Kang MH. Front Oncol 9 635 (2019)
- DNA-PKcs: A Multi-Faceted Player in DNA Damage Response. Yue X, Bai C, Xie D, Ma T, Zhou PK. Front Genet 11 607428 (2020)
- Emerging Perspectives on DNA Double-strand Breaks in Neurodegenerative Diseases. Zhu LS, Wang DQ, Cui K, Liu D, Zhu LQ. Curr Neuropharmacol 17 1146-1157 (2019)
- Holding it together: DNA end synapsis during non-homologous end joining. Loparo JJ. DNA Repair (Amst) 130 103553 (2023)
- How to fix DNA breaks: new insights into the mechanism of non-homologous end joining. Vogt A, He Y, Lees-Miller SP. Biochem Soc Trans 51 1789-1800 (2023)
- Regulation of DNA Double-Strand Break Repair by Non-Coding RNAs. Thapar R. Molecules 23 (2018)
- Share and share alike: the role of Tra1 from the SAGA and NuA4 coactivator complexes. Cheung ACM, Díaz-Santín LM. Transcription 10 37-43 (2019)
- Structural Biology of the HEAT-Like Repeat Family of DNA Glycosylases. Shi R, Shen XX, Rokas A, Eichman BF. Bioessays 40 e1800133 (2018)
- Structural insights into the role of DNA-PK as a master regulator in NHEJ. Chen S, Lees-Miller JP, He Y, Lees-Miller SP. Genome Instab Dis 2 195-210 (2021)
- Targeting the DNA Damage Response Machinery for Lung Cancer Treatment. Venugopala KN. Pharmaceuticals (Basel) 15 1475 (2022)
- The Role of Protein Arginine Methyltransferases in DNA Damage Response. Brobbey C, Liu L, Yin S, Gan W. Int J Mol Sci 23 9780 (2022)
- The TFIIS N-terminal domain (TND): a transcription assembly module at the interface of order and disorder. Cermakova K, Veverka V, Hodges HC. Biochem Soc Trans 51 125-135 (2023)
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- Structures of closed and open conformations of dimeric human ATM. Baretić D, Pollard HK, Fisher DI, Johnson CM, Santhanam B, Truman CM, Kouba T, Fersht AR, Phillips C, Williams RL. Sci Adv 3 e1700933 (2017)
- DNA-PKcs phosphorylation at the T2609 cluster alters the repair pathway choice during immunoglobulin class switch recombination. Crowe JL, Wang XS, Shao Z, Lee BJ, Estes VM, Zha S. Proc Natl Acad Sci U S A 117 22953-22961 (2020)
- Structure of the transcription activator target Tra1 within the chromatin modifying complex SAGA. Sharov G, Voltz K, Durand A, Kolesnikova O, Papai G, Myasnikov AG, Dejaegere A, Ben Shem A, Schultz P. Nat Commun 8 1556 (2017)
- Dissection of DNA double-strand-break repair using novel single-molecule forceps. Wang JL, Duboc C, Wu Q, Ochi T, Liang S, Tsutakawa SE, Lees-Miller SP, Nadal M, Tainer JA, Blundell TL, Strick TR. Nat. Struct. Mol. Biol. 25 482-487 (2018)
- A Mechanism to Minimize Errors during Non-homologous End Joining. Stinson BM, Moreno AT, Walter JC, Loparo JJ. Mol Cell 77 1080-1091.e8 (2020)
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- 3.9 Å structure of the yeast Mec1-Ddc2 complex, a homolog of human ATR-ATRIP. Wang X, Ran T, Zhang X, Xin J, Zhang Z, Wu T, Wang W, Cai G. Science 358 1206-1209 (2017)
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- Structural insights into inhibitor regulation of the DNA repair protein DNA-PKcs. Liang S, Thomas SE, Chaplin AK, Hardwick SW, Chirgadze DY, Blundell TL. Nature 601 643-648 (2022)
- C-Terminal Extensions of Ku70 and Ku80 Differentially Influence DNA End Binding Properties. Inagawa T, Wennink T, Lebbink JHG, Keijzers G, Florea BI, Verkaik NS, van Gent DC. Int J Mol Sci 21 E6725 (2020)
- Cryo-EM visualization of DNA-PKcs structural intermediates in NHEJ. Chen S, Vogt A, Lee L, Naila T, McKeown R, Tomkinson AE, Lees-Miller SP, He Y. Sci Adv 9 eadg2838 (2023)
- Human DNA-dependent protein kinase activation mechanism. Liang S, Blundell TL. Nat Struct Mol Biol 30 140-147 (2023)
- The recent advances in non-homologous end-joining through the lens of lymphocyte development. Wang XS, Lee BJ, Zha S. DNA Repair (Amst) 94 102874 (2020)
- A central role for a region in the middle. Stuttfeld E, Imseng S, Maier T. Elife 6 (2017)
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- Autophosphorylation transforms DNA-PK from protecting to processing DNA ends. Liu L, Chen X, Li J, Wang H, Buehl CJ, Goff NJ, Meek K, Yang W, Gellert M. Mol Cell 82 177-189.e4 (2022)
- Cryo-EM structure of human ATR-ATRIP complex. Rao Q, Liu M, Tian Y, Wu Z, Hao Y, Song L, Qin Z, Ding C, Wang HW, Wang J, Xu Y. Cell Res. 28 143-156 (2018)
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- Structure of the human ATM kinase and mechanism of Nbs1 binding. Warren C, Pavletich NP. Elife 11 e74218 (2022)
- Systematic comparison and prediction of the effects of missense mutations on protein-DNA and protein-RNA interactions. Jiang Y, Liu HF, Liu R. PLoS Comput Biol 17 e1008951 (2021)
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- A functional enrichment test for molecular convergent evolution finds a clear protein-coding signal in echolocating bats and whales. Marcovitz A, Turakhia Y, Chen HI, Gloudemans M, Braun BA, Wang H, Bejerano G. Proc. Natl. Acad. Sci. U.S.A. 116 21094-21103 (2019)
- CRL4ADTL degrades DNA-PKcs to modulate NHEJ repair and induce genomic instability and subsequent malignant transformation. Feng M, Wang Y, Bi L, Zhang P, Wang H, Zhao Z, Mao JH, Wei G. Oncogene 40 2096-2111 (2021)
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- Formation of a structurally-stable conformation by the intrinsically disordered MYC:TRRAP complex. Feris EJ, Hinds JW, Cole MD. PLoS ONE 14 e0225784 (2019)
- Genotoxic stress causes the accumulation of DNA-dependent protein kinase catalytic subunit phosphorylated at serine 2056 at nuclear speckles and alters pre-mRNA alternative splicing. Liu S, Shao Y, Wang Q, Zhai Y, Li X. FEBS Open Bio 9 304-314 (2019)
- Lost in the bloom: DNA-PKcs in green plants. Kumar KRR. Front Plant Sci 14 1231678 (2023)
- Mechanism of auto-inhibition and activation of Mec1ATR checkpoint kinase. Tannous EA, Yates LA, Zhang X, Burgers PM. Nat Struct Mol Biol 28 50-61 (2021)
- PRKDC promotes hepatitis B virus transcription through enhancing the binding of RNA Pol II to cccDNA. Fan Y, Liang Y, Liu Y, Fan H. Cell Death Dis 13 404 (2022)
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- PremPDI estimates and interprets the effects of missense mutations on protein-DNA interactions. Zhang N, Chen Y, Zhao F, Yang Q, Simonetti FL, Li M. PLoS Comput. Biol. 14 e1006615 (2018)
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- XSuLT: a web server for structural annotation and representation of sequence-structure alignments. Ochoa-Montaño B, Blundell TL. Nucleic Acids Res. 45 W381-W387 (2017)
- kinCSM: Using graph-based signatures to predict small molecule CDK2 inhibitors. Zhou Y, Al-Jarf R, Alavi A, Nguyen TB, Rodrigues CHM, Pires DEV, Ascher DB. Protein Sci 31 e4453 (2022)
- mmCSM-NA: accurately predicting effects of single and multiple mutations on protein-nucleic acid binding affinity. Nguyen TB, Myung Y, de Sá AGC, Pires DEV, Ascher DB. NAR Genom Bioinform 3 lqab109 (2021)