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Structural Basis of Transcription: RNA Polymerase II at 2.8 Ångstrom Resolution
Open accessAbstract
Structures of a 10-subunit yeast RNA polymerase II have been derived from two crystal forms at 2.8 and 3.1 angstrom resolution. Comparison of the structures reveals a division of the polymerase into four mobile modules, including a clamp, shown previously to swing over the active center. In the 2.8 angstrom structure, the clamp is in an open state, allowing entry of straight promoter DNA for the initiation of transcription. Three loops extending from the clamp may play roles in RNA unwinding and DNA rewinding during transcription. A 2.8 angstrom difference Fourier map reveals two metal ions at the active site, one persistently bound and the other possibly exchangeable during RNA synthesis. The results also provide evidence for RNA exit in the vicinity of the carboxyl-terminal repeat domain, coupling synthesis to RNA processing by enzymes bound to this domain.
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“A short acidic peptide in the active site of cellular RNA polymerase binds Mg 2+ and positions it for catalysis (Zhang et al. 1999;Cramer et al. 2001).”
From Protocells and RNA Self-Replication (2018) · cites this paper as Cramer et al. 2001
In the citing paper
“RNA polymerase enzymes solve these problems by binding and precisely positioning the metal ion for catalysis (Zhang et al. 1999;Cramer et al. 2001;Robertson and Scott 2007;Shechner et al. 2009).”
From Protocells and RNA Self-Replication (2018) · cites this paper as Cramer et al. 2001
In the citing paper
“Interestingly, the multi-subunit cellular RNA polymerases also use two Mg 2+ ions in the active site, of which the more tightly bound ion is coordinated to three asp residues in a highly conserved NADFDGD peptide sequence [60,61].”
From The eightfold path to non-enzymatic RNA replication (2012) · cites this paper as [61]
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Metadata
- Authors
- Cramer, P., Bushnell, D. A., & Kornberg, R. D.
- Affiliations
- Stanford Medicine (US)
- Corresponding author
- Cramer, Patrick
- Kornberg, Roger D.
- Venue
- Science
- Published
- 2001-06-08
- Volume
- 292
- Issue
- 5523
- Pages
- 1863-1876
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- OpenAlex
- W2074206760
- Cited by
- 1,247
- References
- 71
- Citations by year
- 2026: 18 · 2025: 16 · 2024: 40 · 2023: 29 · 2022: 29 · 2021: 38 · 2020: 38 · 2019: 48 · 2018: 34 · 2017: 51 · 2016: 33 · 2015: 37 · 2014: 50 · 2013: 55 · 2012: 63
- FWCI
- 27.00
- Type
- journal article
- Language
- en
- Open access
- green
- hdl.handle.net
- Licence
- other-oa
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- Max Planck Digital Library (submittedVersion, other-oa)
- GRO (submittedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion, other-oa)
- Funders
- National Institute of General Medical Sciences (GM49985, R01GM049985)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Keywords
- RNA polymerase II, transcription initiation, active site metal ions, RNA unwinding, promoter DNA, crystal structure
- MeSH terms
- Amino Acid Sequence, Binding Sites, DNA, Fungal, Fourier Analysis, Hydrogen Bonding, Magnesium, Metals, Models, Molecular, Molecular Sequence Data, Promoter Regions, Genetic, Protein Conformation, RNA Polymerase II, RNA Processing, Post-Transcriptional, RNA, Fungal, RNA, Messenger, Saccharomyces cerevisiae, Transcription Factors, Transcription, Genetic, Conserved Sequence, Protein Structure, Secondary, Protein Structure, Tertiary, Crystallography, X-Ray, Protein Structure, Quaternary, Protein Subunits
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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