Cryo-EM visualization of DNA-PKcs structural intermediates in NHEJ

Structure of an activated DNA-PK and its implications for NHEJ

(2021) Xuemin Chen et al.   MOLECULAR CELL

Repair of DNA Double-Strand Breaks by the Nonhomologous End Joining Pathway

(2021) Benjamin M. Stinson et al.   Annual Review of Biochemistry

Structural basis of long-range to short-range synaptic transition in NHEJ

(2021) Siyu Chen et al.   NATURE

Cryo-EM of NHEJ supercomplexes provides insights into DNA repair

(2021) Amanda K. Chaplin et al.   MOLECULAR CELL

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

DeepEMhancer: a deep learning solution for cryo-EM volume post-processing

(2021) Ruben Sanchez-Garcia et al.   Communications Biology

Autophosphorylation transforms DNA-PK from protecting to processing DNA ends

(2021) Lan Liu et al.   MOLECULAR CELL

The molecular basis and disease relevance of non-homologous DNA end joining

(2020) Bailin Zhao et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Dimers of DNA-PK create a stage for DNA double-strand break repair

(2020) Amanda K. Chaplin et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Uncovering DNA-PKcs ancient phylogeny, unique sequence motifs and insights for human disease

(2020) James P. Lees-Miller et al.   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

UCSF ChimeraX : Structure visualization for researchers, educators, and developers

(2020) Eric F. Pettersen et al.   PROTEIN SCIENCE

XLF acts as a flexible connector during non-homologous end joining

(2020) Sean M Carney et al.   eLife

Namdinator – automatic molecular dynamics flexible fitting of structural models into cryo-EM and crystallography experimental maps

(2019) Rune Thomas Kidmose et al.   IUCrJ

Dissection of DNA double-strand-break repair using novel single-molecule forceps

(2018) Jing L. Wang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Dissection of DNA double-strand-break repair using novel single-molecule forceps

(2018) Jing L. Wang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps

(2018) Tristan Ian Croll   Acta Crystallographica Section D-Structural Biology

Real-space refinement in PHENIX for cryo-EM and crystallography

(2018) Pavel V. Afonine et al.   Acta Crystallographica Section D-Structural Biology

XLF and APLF bind Ku80 at two remote sites to ensure DNA repair by non-homologous end joining

(2018) Clement Nemoz et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

COSMIC: the Catalogue Of Somatic Mutations In Cancer

(2018) John G Tate et al.   NUCLEIC ACIDS RESEARCH

New tools for automated high-resolution cryo-EM structure determination in RELION-3

(2018) Jasenko Zivanov et al.   eLife

cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination

(2017) Ali Punjani et al.   NATURE METHODS

Addressing preferred specimen orientation in single-particle cryo-EM through tilting

(2017) Yong Zi Tan et al.   NATURE METHODS

DNA-PKcs structure suggests an allosteric mechanism modulating DNA double-strand break repair

(2017) Bancinyane L. Sibanda et al.   SCIENCE

PAXX promotes KU accumulation at DNA breaks and is essential for end-joining in XLF-deficient mice

(2017) Xiangyu Liu et al.   Nature Communications

Structures of closed and open conformations of dimeric human ATM

(2017) Domagoj Baretić et al.   Science Advances

Deficiency of XLF and PAXX prevents DNA double-strand break repair by non-homologous end joining in lymphocytes

(2016) Putzer J. Hung et al.   CELL CYCLE

An Intrinsically Disordered APLF Links Ku, DNA-PKcs, and XRCC4-DNA Ligase IV in an Extended Flexible Non-homologous End Joining Complex

(2016) Michal Hammel et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

PAXX Is an Accessory c-NHEJ Factor that Associates with Ku70 and Has Overlapping Functions with XLF

(2016) Satish K. Tadi et al.   Cell Reports

XLS (c9orf142) is a new component of mammalian DNA double-stranded break repair

(2015) A Craxton et al.   CELL DEATH AND DIFFERENTIATION

CTFFIND4: Fast and accurate defocus estimation from electron micrographs

(2015) Alexis Rohou et al.   JOURNAL OF STRUCTURAL BIOLOGY

PAXX, a paralog of XRCC4 and XLF, interacts with Ku to promote DNA double-strand break repair

(2015) T. Ochi et al.   SCIENCE

Interactome analysis identifies a new paralogue of XRCC4 in non-homologous end joining DNA repair pathway

(2015) Mengtan Xing et al.   Nature Communications

PhosphoSitePlus, 2014: mutations, PTMs and recalibrations

(2014) Peter V. Hornbeck et al.   NUCLEIC ACIDS RESEARCH

mTOR kinase structure, mechanism and regulation

(2013) Haijuan Yang et al.   NATURE

Quantifying the local resolution of cryo-EM density maps

(2013) Alp Kucukelbir et al.   NATURE METHODS

Prevention of overfitting in cryo-EM structure determination

(2012) Sjors H W Scheres et al.   NATURE METHODS

Live cell imaging of XLF and XRCC4 reveals a novel view of protein assembly in the non-homologous end-joining pathway

(2011) Ken-ichi Yano et al.   CELL CYCLE

Features and development ofCoot

(2010) P. Emsley et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Protein Phosphatase 6 Interacts with the DNA-Dependent Protein Kinase Catalytic Subunit and Dephosphorylates  -H2AX

(2010) P. Douglas et al.   MOLECULAR AND CELLULAR BIOLOGY

Appion: An integrated, database-driven pipeline to facilitate EM image processing

(2009) Gabriel C. Lander et al.   JOURNAL OF STRUCTURAL BIOLOGY

DoG Picker and TiltPicker: Software tools to facilitate particle selection in single particle electron microscopy

(2009) N.R. Voss et al.   JOURNAL OF STRUCTURAL BIOLOGY

DNA-PK and ATM phosphorylation sites in XLF/Cernunnos are not required for repair of DNA double strand breaks

(2008) Y YU et al.   DNA REPAIR