ArticleThe Journal of biological chemistry2009
Structure of the 12-subunit RNA polymerase II refined with the aid of anomalous diffraction data.
Article in The Journal of biological chemistry, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Article
- KSHV-encoded LANA bypasses transcriptional block through the stabilization of RNA Pol II in hypoxia.mBio · 2024Article
- Modeling DNA Opening in the Eukaryotic Transcription Initiation Complexes via Coarse-Grained Models.Frontiers in molecular biosciences · 2021Article
- Source of the Fitness Defect in Rifamycin-Resistant Mycobacterium tuberculosis RNA Polymerase and the Mechanism of Compensation by Mutations in the β' Subunit.Antimicrobial agents and chemotherapy · 2018Article
- Can I solve my structure by SAD phasing? Planning an experiment, scaling data and evaluating the useful anomalous correlation and anomalous signal.Acta crystallographica. Section D, Structural biology · 2016Article
- Crystal Structure of a Transcribing RNA Polymerase II Complex Reveals a Complete Transcription Bubble.Molecular cell · 2015Article
- The non-coding B2 RNA binds to the DNA cleft and active-site region of RNA polymerase II.Journal of molecular biology · 2013Article
- Correct assembly of RNA polymerase II depends on the foot domain and is required for multiple steps of transcription in Saccharomyces cerevisiae.Molecular and cellular biology · 2013Article
- An integrated chemical cross-linking and mass spectrometry approach to study protein complex architecture and function.Molecular & cellular proteomics : MCP · 2012Article
- The conserved foot domain of RNA pol II associates with proteins involved in transcriptional initiation and/or early elongation.Genetics · 2011Article
- Interaction of RNA polymerase II fork loop 2 with downstream non-template DNA regulates transcription elongation.The Journal of biological chemistry · 2011Article
- RNA polymerase II conserved protein domains as platforms for protein-protein interactions.Transcription · 2011Article
- A novel N-acetylglutamate synthase architecture revealed by the crystal structure of the bifunctional enzyme from Maricaulis maris.PloS one · 2011Article
- A dual interface determines the recognition of RNA polymerase II by RNA capping enzyme.The Journal of biological chemistry · 2010Article
- Forks, pincers, and triggers: the tools for nucleotide incorporation and translocation in multi-subunit RNA polymerases.Current opinion in structural biology · 2009Review
- Schizosacharomyces pombe RNA polymerase II at 3.6-A resolution.Proceedings of the National Academy of Sciences of the United States of America · 2009Article
- Transcription termination by the eukaryotic RNA polymerase III.Biochimica et biophysica actaReview
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5 authors.
Funding
Abstract
RNA polymerase II (Pol II) is the central enzyme of eukaryotic gene expression machinery. Complete definition of the three-dimensional structure of Pol II is essential for understanding the mechanisms that regulate transcription via protein-protein interactions within the Pol II apparatus. To date a series of Pol II-related crystal structures have been reported. However, certain peptide regions, including several that are implicated to interact with regulatory factors, remain obscure. Here we describe conformations for two such regions that are close to the Pol II surface and assume seemingly flexible loop structures. One is located in the TFIIF-interacting Protrusion domain, whereas the other is in the TFIIE-interacting Clamp domain. This structural definition was aided by the application of an advanced crystallographic refinement approach that utilizes the single anomalous diffraction (SAD) from zinc ions bound intrinsically in Pol II. The SAD-based strategy allowed the 12-subunit Pol II model to be fully refined up to 3.8 A with excellent stereochemical properties, demonstrating the effectiveness of the SAD approach for the refinement of large structures at low-to-moderate resolutions. Our results also define additional components of the free Pol II, including the functionally critical Fork Loop-1 and Fork Loop-2 elements. As such, this refined Pol II model provides the most complete structural reference for future analyses of complex structures formed between Pol II and its regulatory factors.
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