Evidence map›Paper›PMID 33412091›Full record

ArticleStructure (London, England : 1993)2021

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

Morgan Hepburn, Daniel J Saltzberg, Linda Lee, Shujuan Fang, Claire Atkinson, Natalie C J Strynadka, Andrej Sali, Susan P Lees-Miller, David C Schriemer

Abstract read
In one paragraph

Article in Structure (London, England : 1993), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.

0numbers the graph read from it
0cells of the map it votes in
10citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

10 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. Review
  5. Article
  6. Article
  7. Article
  8. Review
  9. Tools for Decoding Ubiquitin Signaling in DNA Repair.Frontiers in cell and developmental biology · 2021
    Review
  10. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

9 authors.

Morgan HepburnDepartment of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada.
Daniel J SaltzbergDepartment of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Sciences, and California Institute for Quantitative Biomedical Sciences, University of California, San Francisco, CA 94158, USA.
Linda LeeDepartment of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada.
Shujuan FangDepartment of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada.
Claire AtkinsonDepartment of Biochemistry and Molecular Biology and High-Resolution Macromolecular Electron Microscopy Facility, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.
Natalie C J StrynadkaDepartment of Biochemistry and Molecular Biology and High-Resolution Macromolecular Electron Microscopy Facility, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.
Andrej SaliDepartment of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Sciences, and California Institute for Quantitative Biomedical Sciences, University of California, San Francisco, CA 94158, USA.
Susan P Lees-MillerDepartment of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada; Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB, Canada.
David C SchriemerDepartment of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada; Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB, Canada; Department of Chemistry, University of Calgary, Calgary, AB, Canada. Electronic address: dschriem@ucalgary.ca.

Funding

Transcription-Coupled & Replication-Associated Excision RepairP01CA092584 · NCI · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · PI WALTER J. CHAZIN · 2001 to 2026
$89.6M
TR&D Project 4. The Imaging Stage: Multiscale Spatiotemporal Modeling of Macromolecular Systems in Cellular NeighborhoodsP41GM109824 · NIGMS · ROCKEFELLER UNIVERSITY · PI ROUT, MICHAEL P · 2014 to 2023
$18.8M
IMP: Software for Hybrid Determination of Macromolecular Assembly StructuresR01GM083960 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI SALI, ANDREJ · 2008 to 2024
$5.2M
High Performance Computer for Computational BiosciencesS10OD021596 · OD · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI SALI, ANDREJ · 2016 to 2016
$443k
NCI NIH HHS P01 CA092584NIGMS NIH HHS P41 GM109824NIGMS NIH HHS R01 GM083960NIH HHS S10 OD021596
6 · The paper itself

Abstract

In the non-homologous end-joining (NHEJ) of a DNA double-strand break, DNA ends are bound and protected by DNA-PK, which synapses across the break to tether the broken ends and initiate repair. There is little clarity surrounding the nature of the synaptic complex and the mechanism governing the transition to repair. We report an integrative structure of the synaptic complex at a precision of 13.5 Å, revealing a symmetric head-to-head arrangement with a large offset in the DNA ends and an extensive end-protection mechanism involving a previously uncharacterized plug domain. Hydrogen/deuterium exchange mass spectrometry identifies an allosteric pathway connecting DNA end-binding with the kinase domain that places DNA-PK under tension in the kinase-active state. We present a model for the transition from end-protection to repair, where the synaptic complex supports hierarchical processing of the ends and scaffold assembly, requiring displacement of the catalytic subunit and tension release through kinase activity.

Indexed as

Binding SitesDNA-Activated Protein KinaseDNA End-Joining RepairHeLa CellsHoloenzymesHumansMolecular Docking SimulationProtein BindingSynaptonemal ComplexDNA-Activated Protein KinaseHoloenzymescrosslinking mass spectrometryDNA-PKDNA repairhydrogen/deuterium exchangemodelingnon-homologous end-joiningstructuresynaptic complex

Identifiers

PMID33412091
PMCPMC8675206

What OpenQuestion holds

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Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.