Evidence map›Paper›PMID 34099686›Full record

ArticleNature communications2021

Cryo-EM structure of TFIIH/Rad4-Rad23-Rad33 in damaged DNA opening in nucleotide excision repair.

Trevor van Eeuwen, Yoonjung Shim, Hee Jong Kim, Tingting Zhao, Shrabani Basu, Benjamin A Garcia, Craig D Kaplan, Jung-Hyun Min, Kenji Murakami

Abstract read
In one paragraph

Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.

0numbers the graph read from it
0cells of the map it votes in
28citing 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

28 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. Review
  5. A new crystal form of the DNA-free full-length XPD helicase from Thermoplasma acidophilum.Acta crystallographica. Section F, Structural biology communications · 2026
    Article
  6. Review
  7. Article
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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.

Trevor van EeuwenDepartment of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.ORCID 0000-0003-0549-1702
Yoonjung ShimDepartment of Chemistry and Biochemistry, Baylor University, Waco, TX, USA.
Hee Jong KimDepartment of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Tingting ZhaoDepartment of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA.
Shrabani BasuDepartment of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA.ORCID 0000-0001-5096-5490
Benjamin A GarciaDepartment of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Craig D KaplanDepartment of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA.ORCID 0000-0002-7518-695X
Jung-Hyun MinDepartment of Chemistry and Biochemistry, Baylor University, Waco, TX, USA. JungHyun_Min@baylor.edu.ORCID 0000-0002-4221-9321
Kenji MurakamiDepartment of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. kenjim@pennmedicine.upenn.edu.ORCID 0000-0002-2017-5575

Funding

NCCAT: National Center for CryoEM Access and Training- Supplement for Windows 10 and FFIU24GM129539 · NIGMS · NEW YORK STRUCTURAL BIOLOGY CENTER · PI DE MARCO, ALEX, KIEFT, JEFFREY S · 2018 to 2023
$53.9M
STRUCTURAL BASIS FOR EPIGENETICS IN AGING AND LONGEVITYP01AG031862 · NIA · WISTAR INSTITUTE · PI ADAMS, PETER D. · 2008 to 2022
$28.3M
Shared Resources Core 2: Quantitative Proteomics CoreP01CA196539 · NCI · ROCKEFELLER UNIVERSITY · PI MUIR, TOM · 2015 to 2024
$17.6M
STRUCTURAL BIOLOGY TRAINING PROGRAMT32GM008275 · NIGMS · UNIVERSITY OF PENNSYLVANIA · PI WAND, A. JOSHUA · 1988 to 2018
$6.0M
Viral modulation of epitranscriptomic mechanismsR01AI118891 · NIAID · WASHINGTON UNIVERSITY · PI GARCIA, BENJAMIN A, WEITZMAN, MATTHEW D. · 2015 to 2025
$5.4M
Functional and structural studies of the transition from transcription initiation to elongationR01GM123233 · NIGMS · UNIVERSITY OF PENNSYLVANIA · PI MURAKAMI, KENJI · 2017 to 2025
$3.6M
Predoctoral Training at the Chemistry-Biology InterfaceT32GM071339 · NIGMS · WISTAR INSTITUTE · PI MARMORSTEIN, RONEN, SPEICHER, DAVID W. · 2005 to 2019
$3.2M
"Mechanisms of RNA Polymerase II initiation"R01GM120450 · NIGMS · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI KAPLAN, CRAIG · 2016 to 2019
$1.7M
Arylamine DNA adduct recognition in eukaryotic nucleotide excision repairR21ES028384 · NIEHS · UNIVERSITY OF RHODE ISLAND · PI CHO, BONGSUP P, MIN, JUNG-HYUN · 2017 to 2018
$443k
Computational Resource for Structural Biology and Molecular BiophysicsS10OD023592 · OD · UNIVERSITY OF PENNSYLVANIA · PI SHARP, KIM A · 2017 to 2017
$402k
NCI NIH HHS P01 CA196539NIAID NIH HHS R01 AI118891NIA NIH HHS P01 AG031862NIEHS NIH HHS R21 ES028384NIGMS NIH HHS R01 GM120450NIGMS NIH HHS R01 GM123233NIGMS NIH HHS T32 GM008275NIGMS NIH HHS T32 GM071339NIGMS NIH HHS U24 GM129539NIH HHS S10 OD023592
6 · The paper itself

Abstract

The versatile nucleotide excision repair (NER) pathway initiates as the XPC-RAD23B-CETN2 complex first recognizes DNA lesions from the genomic DNA and recruits the general transcription factor complex, TFIIH, for subsequent lesion verification. Here, we present a cryo-EM structure of an NER initiation complex containing Rad4-Rad23-Rad33 (yeast homologue of XPC-RAD23B-CETN2) and 7-subunit coreTFIIH assembled on a carcinogen-DNA adduct lesion at 3.9-9.2 Å resolution. A ~30-bp DNA duplex could be mapped as it straddles between Rad4 and the Ssl2 (XPB) subunit of TFIIH on the 3' and 5' side of the lesion, respectively. The simultaneous binding with Rad4 and TFIIH was permitted by an unwinding of DNA at the lesion. Translocation coupled with torque generation by Ssl2 and Rad4 would extend the DNA unwinding at the lesion and deliver the damaged strand to Rad3 (XPD) in an open form suitable for subsequent lesion scanning and verification.

Indexed as

Cryoelectron MicroscopyDNA DamageDNA RepairDNADNA AdductsDNA-Binding ProteinsDNA HelicasesSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsTranscription Factor TFIIHDNADNA AdductsDNA-Binding ProteinsDNA HelicasesRAD23 protein, S cerevisiaeRad33 protein, S cerevisiaeRad3 protein, S cerevisiaeRad4 protein, S cerevisiaeSaccharomyces cerevisiae ProteinsSSL2 protein, S cerevisiaeTranscription Factor TFIIH

Identifiers

PMID34099686
PMCPMC8184850

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Registered trials

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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.