The active DNA-PK holoenzyme occupies a tensed state in a staggered synaptic complex

Structural insights into the critical DNA damage sensors DNA-PKcs, ATM and ATR

(2019) Domagoj Baretic et al.   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

SSEThread: Integrative threading of the DNA-PKcs sequence based on data from chemical cross-linking and hydrogen deuterium exchange

(2019) Daniel J. Saltzberg et al.   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

Cryo-EM Structure of Nucleotide-Bound Tel1ATM Unravels the Molecular Basis of Inhibition and Structural Rationale for Disease-Associated Mutations

(2019) Luke A. Yates et al.   STRUCTURE

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

A single XLF dimer bridges DNA ends during nonhomologous end joining

(2018) Thomas G. W. Graham et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The PRIDE database and related tools and resources in 2019: improving support for quantification data

(2018) Yasset Perez-Riverol et al.   NUCLEIC ACIDS RESEARCH

Integrative structure modeling with the Integrative Modeling Platform

(2017) Benjamin Webb et al.   PROTEIN SCIENCE

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

(2017) Bancinyane L. Sibanda et al.   SCIENCE

PDB-Dev: a Prototype System for Depositing Integrative/Hybrid Structural Models

(2017) Stephen K. Burley et al.   STRUCTURE

DNA Ligase IV Guides End-Processing Choice during Nonhomologous End Joining

(2017) Michael P. Conlin et al.   Cell Reports

Structure of the human dimeric ATM kinase

(2016) Wilson C. Y. Lau et al.   CELL CYCLE

Different DNA End Configurations Dictate Which NHEJ Components Are Most Important for Joining Efficiency

(2016) Howard H. Y. Chang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes

(2016) G.C.P. van Zundert et al.   JOURNAL OF MOLECULAR BIOLOGY

High Sensitivity Crosslink Detection Coupled With Integrative Structure Modeling in the Mass Spec Studio

(2016) Vladimir Sarpe et al.   MOLECULAR & CELLULAR PROTEOMICS

Two-Stage Synapsis of DNA Ends during Non-homologous End Joining

(2016) Thomas G.W. Graham et al.   MOLECULAR CELL

Achieving selectivity in space and time with DNA double-strand-break response and repair: molecular stages and scaffolds come with strings attached

(2016) S. Liang et al.   STRUCTURAL 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

Recombinant Nepenthesin II for Hydrogen/Deuterium Exchange Mass Spectrometry

(2015) Menglin Yang et al.   ANALYTICAL CHEMISTRY

Xlink Analyzer: Software for analysis and visualization of cross-linking data in the context of three-dimensional structures

(2015) Jan Kosinski et al.   JOURNAL OF STRUCTURAL BIOLOGY

Differential Phosphorylation of DNA-PKcs Regulates the Interplay between End-Processing and End-Ligation during Nonhomologous End-Joining

(2015) Wenxia Jiang et al.   MOLECULAR CELL

A strategy for dissecting the architectures of native macromolecular assemblies

(2015) Yi Shi et al.   NATURE METHODS

xVis: a web server for the schematic visualization and interpretation of crosslink-derived spatial restraints

(2015) Maximilian Grimm et al.   NUCLEIC ACIDS RESEARCH

The DNA-dependent protein kinase: A multifunctional protein kinase with roles in DNA double strand break repair and mitosis

(2015) Nicholas Jette et al.   PROGRESS IN BIOPHYSICS & MOLECULAR 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

Toward Standardizing Deuterium Content Reporting in Hydrogen Exchange-MS

(2014) Joey G. Sheff et al.   ANALYTICAL CHEMISTRY

Molecular Architecture of the 40S⋅eIF1⋅eIF3 Translation Initiation Complex

(2014) Jan P. Erzberger et al.   CELL

Uncertainty in integrative structural modeling

(2014) Dina Schneidman-Duhovny et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Structural Characterization by Cross-linking Reveals the Detailed Architecture of a Coatomer-related Heptameric Module from the Nuclear Pore Complex

(2014) Yi Shi et al.   MOLECULAR & CELLULAR PROTEOMICS

Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ

(2014) Jürgen Cox et al.   MOLECULAR & CELLULAR PROTEOMICS

Unraveling the Complexities of DNA-Dependent Protein Kinase Autophosphorylation

(2014) J. A. Neal et al.   MOLECULAR AND CELLULAR BIOLOGY

The fidelity of the ligation step determines how ends are resolved during nonhomologous end joining

(2014) Crystal A. Waters et al.   Nature Communications

pyRMSD: a Python package for efficient pairwise RMSD matrix calculation and handling

(2013) Víctor A. Gil et al.   BIOINFORMATICS

A noncatalytic function of the ligation complex during nonhomologous end joining

(2013) Jessica Cottarel et al.   JOURNAL OF CELL BIOLOGY

Putting the Pieces Together: Integrative Modeling Platform Software for Structure Determination of Macromolecular Assemblies

(2012) Daniel Russel et al.   PLOS BIOLOGY

XRCC4 Protein Interactions with XRCC4-like Factor (XLF) Create an Extended Grooved Scaffold for DNA Ligation and Double Strand Break Repair

(2011) Michal Hammel et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Putative binding modes of Ku70-SAP domain with double strand DNA: a molecular modeling study

(2011) Shaowen Hu et al.   JOURNAL OF MOLECULAR MODELING

N-terminal constraint activates the catalytic subunit of the DNA-dependent protein kinase in the absence of DNA or Ku

(2011) K. Meek et al.   NUCLEIC ACIDS RESEARCH

Structural characterization of filaments formed by human Xrcc4-Cernunnos/XLF complex involved in nonhomologous DNA end-joining

(2011) V. Ropars et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ku and DNA-dependent Protein Kinase Dynamic Conformations and Assembly Regulate DNA Binding and the Initial Non-homologous End Joining Complex

(2009) Michal Hammel et al.   JOURNAL OF BIOLOGICAL CHEMISTRY