Evidence map›Paper›PMID 31582849›Full record

ArticleNature structural & molecular biology2019

Cryo-EM structure and dynamics of eukaryotic DNA polymerase δ holoenzyme.

Rinku Jain, William J Rice, Radhika Malik, Robert E Johnson, Louise Prakash, Satya Prakash, Iban Ubarretxena-Belandia, Aneel K Aggarwal

Open access · greenAbstract read
In one paragraph

Article in Nature structural & molecular biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.

0numbers the graph read from it
0cells of the map it votes in
33citing papers in PubMed
2.9field-weighted citation impact, top 8% of its field
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

33 citing papers in PubMed, 52 citations in OpenAlex.

  1. Article
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  7. POLD3 as Controller of Replicative DNA Repair.International journal of molecular sciences · 2024
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  9. Article
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  15. Article
  16. Structural and Molecular Kinetic Features of Activities of DNA Polymerases.International journal of molecular sciences · 2022
    Review
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  20. Article
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

8 authors at 4 institutions in 2 countries.

Rinku JainDepartment of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA. rinku.jain@mssm.edu.ORCID http://orcid.org/0000-0003-2285-7809
William J RiceSimons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA.
Radhika MalikDepartment of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
Robert E JohnsonDepartment of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA.
Louise PrakashDepartment of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA.
Satya PrakashDepartment of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA.
Iban Ubarretxena-BelandiaDepartment of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
Aneel K AggarwalDepartment of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA. aneel.aggarwal@mssm.edu.ORCID http://orcid.org/0000-0003-4389-0173
Icahn School of Medicine at Mount Sinai · USThe University of Texas Medical Branch at Galveston · USIkerbasque · ESNew York Structural Biology Center · US

Funding

TRD #3: An automated and streamlined pipeline for in-situ molecular microscopyP41GM103310 · NIGMS · SCRIPPS RESEARCH INSTITUTE, THE · PI DE MARCO, ALEX, KIEFT, JEFFREY S · 2012 to 2021
$14.7M
Resource for Biocomputing Visualization and InformaticsP41GM103311 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI FERRIN, THOMAS E · 2012 to 2017
$8.2M
Structure and Specificity of Restriction-Modification (R-M) SystemsR35GM131780 · NIGMS · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI ANEEL K. AGGARWAL · 2019 to 2026
$3.4M
Effects of PS1FAD mutations on PS1-NMDAR association, necroptosis and electrophysiology.RF1AG008200 · NIA · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI ROBAKIS, NIKOLAOS K · 2018 to 2018
$2.8M
Dual-Beam Scanning Electron Microscope for New York Structural Biology CenterS10RR029300 · NCRR · NEW YORK STRUCTURAL BIOLOGY CENTER · PI STOKES, DAVID L. · 2010 to 2010
$2.0M
Roles of DNA polymerases delta and epsilon in replication, repair, and genomic fidelityR01GM129689 · NIGMS · UNIVERSITY OF TEXAS MED BR GALVESTON · PI PRAKASH, SATYA · 2018 to 2021
$1.3M
Acquisition of Detector for JEOL 3200 FSC Electron MicroscopeS10OD019994 · OD · NEW YORK STRUCTURAL BIOLOGY CENTER · PI CARRAGHER, BRIDGET OLIVIA · 2015 to 2015
$600k
Acquisition of an electron cryo-microscope for structural biologyS10RR026473 · NCRR · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI UBARRETXENA, IBAN · 2011 to 2011
$500k
NCRR NIH HHS S10 RR026473NCRR NIH HHS S10 RR029300NIA NIH HHS RF1 AG008200NIGMS NIH HHS P41 GM103310NIGMS NIH HHS P41 GM103311NIGMS NIH HHS R01 GM129689NIGMS NIH HHS R35 GM131780NIH HHS S10 OD019994
6 · The paper itself

Abstract

DNA polymerase δ (Polδ) plays pivotal roles in eukaryotic DNA replication and repair. Polδ is conserved from yeast to humans, and mutations in human Polδ have been implicated in various cancers. Saccharomyces cerevisiae Polδ consists of catalytic Pol3 and the regulatory Pol31 and Pol32 subunits. Here, we present the near atomic resolution (3.2 Å) cryo-EM structure of yeast Polδ holoenzyme in the act of DNA synthesis. The structure reveals an unexpected arrangement in which the regulatory subunits (Pol31 and Pol32) lie next to the exonuclease domain of Pol3 but do not engage the DNA. The Pol3 C-terminal domain contains a 4Fe-4S cluster and emerges as the keystone of Polδ assembly. We also show that the catalytic and regulatory subunits rotate relative to each other and that this is an intrinsic feature of the Polδ architecture. Collectively, the structure provides a framework for understanding DNA transactions at the replication fork.

Indexed as

Amino Acid SequenceCryoelectron MicroscopyDNA-Directed DNA PolymeraseDNA, FungalDNA Polymerase IIIMolecular Docking SimulationProtein BindingProtein ConformationSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsDNA-Directed DNA PolymeraseDNA, FungalDNA Polymerase IIIPOL31 protein, S cerevisiaePol32 protein, S cerevisiaePOL3 protein, S cerevisiaeSaccharomyces cerevisiae Proteins

Identifiers

PMID31582849
PMCPMC7309520
OpenAlexW2977632608

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.