Evidence map›Paper›PMID 39190355›Full record

ArticleProceedings of the National Academy of Sciences of the United States of America2024

Structural basis of transcription: RNA polymerase II substrate binding and metal coordination using a free-electron laser.

Guowu Lin, Christopher O Barnes, Simon Weiss, Bercem Dutagaci, Chenxi Qiu, Michael Feig, Jihnu Song, Artem Lyubimov, Aina E Cohen, Craig D Kaplan and 1 more

Abstract read
In one paragraph

Article in Proceedings of the National Academy of Sciences of the United States of America, 2024. 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. Article
  5. Article
  6. Preparing for successful protein crystallization experiments.Acta crystallographica. Section F, Structural biology communications · 2025
    Article
  7. Article
  8. Review
  9. Article
  10. Structural basis of transcription: RNA polymerase II substrate binding and metal coordination using a free-electron laser.Proceedings of the National Academy of Sciences of the United States of America · 2024
    Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

11 authors.

Guowu Lin *Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261.
Christopher O Barnes *Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125.ORCID 0000-0003-2754-5951
Simon Weiss *Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261.
Bercem DutagaciDepartment of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824.ORCID 0000-0003-0333-5757
Chenxi QiuDepartment of Genetics, Harvard Medical School, Boston, MA 02115.
Michael FeigDepartment of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824.ORCID 0000-0001-9380-6422
Jihnu SongStanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025.
Artem LyubimovStanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025.ORCID 0000-0002-2089-1870
Aina E CohenStanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025.ORCID 0000-0003-2414-9427
Craig D KaplanDepartment of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260.ORCID 0000-0002-7518-695X
Guillermo CaleroDepartment of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261.ORCID 0000-0003-3730-4676

Funding

A Synchrotron Radiation Structural Biology ResourcesP30GM133894 · NIGMS · STANFORD UNIVERSITY · PI Thomas Michael Weiss · 2020 to 2026
$43.3M
Project 3. IntegrationU54AI170791 · NIAID · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI Jacek Skowronski · 2022 to 2026
$30.6M
Structural Dynamics at LCLSP41GM139687 · NIGMS · STANFORD UNIVERSITY · PI BOUTET, SEBASTIEN · 2021 to 2025
$7.5M
Mechanisms of RNA Polymerase II transcriptionR35GM144116 · NIGMS · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI Craig Kaplan · 2022 to 2026
$3.4M
Mechanism and Regulation of RNA Polymerase II ElongationR01GM097260 · NIGMS · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI KAPLAN, CRAIG · 2011 to 2020
$3.3M
Modeling and dynamics of biomolecules on cellular scalesR35GM126948 · NIGMS · MICHIGAN STATE UNIVERSITY · PI Michael Feig · 2018 to 2026
$3.2M
Structural Studies of RNA Polymerase II Transcription Initiation and ElongationR01GM112686 · NIGMS · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI CALERO, GUILLERMO ALBERTO · 2015 to 2024
$2.8M
High-end X-ray Detector System for Femtosecond CrystallographyS10OD023453 · OD · STANFORD UNIVERSITY · PI BOUTET, SEBASTIEN · 2017 to 2017
$1.7M
Molecular basis of uterine cellular interactionsR01CA112686 · NCI · MOUNT SINAI SCHOOL OF MEDICINE OF NYU · PI SASSOON, DAVID A · 2004 to 2008
$1.5M
HHS | NIH | NCI | CCR | Basic Research Laboratory (BRL) R01GM097260HHS | NIH | NCI | CCR | Basic Research Laboratory (BRL) R01GM112686HHS | NIH | NCI | CCR | Basic Research Laboratory (BRL) R35GM126948HHS | NIH | NCI | CCR | Basic Research Laboratory (BRL) R35GM144116NIAID NIH HHS U54 AI170791NIGMS NIH HHS P30 GM133894NIGMS NIH HHS P41 GM139687NIGMS NIH HHS R01 GM097260NIGMS NIH HHS R01 GM112686NIGMS NIH HHS R35 GM126948NIGMS NIH HHS R35 GM144116NIH HHS S10 OD023453
6 · The paper itself

Abstract

Catalysis and translocation of multisubunit DNA-directed RNA polymerases underlie all cellular mRNA synthesis. RNA polymerase II (Pol II) synthesizes eukaryotic pre-mRNAs from a DNA template strand buried in its active site. Structural details of catalysis at near-atomic resolution and precise arrangement of key active site components have been elusive. Here, we present the free-electron laser (FEL) structures of a matched ATP-bound Pol II and the hyperactive Rpb1 T834P bridge helix (BH) mutant at the highest resolution to date. The radiation-damage-free FEL structures reveal the full active site interaction network, including the trigger loop (TL) in the closed conformation, bonafide occupancy of both site A and B Mg

Indexed as

Catalytic DomainMagnesiumMolecular Dynamics SimulationRNA Polymerase IITranscription, GeneticAdenosine TriphosphateBinding SitesElectronsLasersProtein BindingProtein ConformationAdenosine TriphosphateMagnesiumRNA Polymerase IIcatalytic mechanismsmagnesium chemistryRNA polymerase IItranscriptionXFEL

Identifiers

PMID39190355
PMCPMC11388330

What Socratic holds

Textmetadata
LicenceCC BY-NC-ND
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 Socratic graph.