<scp>UCSF ChimeraX</scp>: Structure visualization for researchers, educators, and developers

Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C.; Meng, Elaine C.; Couch, Gregory S.; Croll, Tristan I.; Morris, John H.; Ferrin, Thomas E.

doi:10.1002/pro.3943

Cited by 5,813 publications

(4,695 citation statements)

References 42 publications

Supporting

Mentioning

4,158

Contrasting

Unclassified

Order By: Relevance

“…To superpose the structures of RNAP, we used the αNTDs and the catalytic domains (DPBB domains from the β and β’ subunits) of RNAP as references. Figures were prepared by ChimeraX 58 and Pymol.…”

Section: Methodsmentioning

confidence: 99%

Structural basis of ribosomal RNA transcription regulation

et al. 2021

View full text Add to dashboard Cite

Ribosomal RNA (rRNA) is most highly expressed in rapidly growing bacteria and is drastically downregulated under stress conditions by the global transcriptional regulator DksA and the alarmone ppGpp. Here, we determined cryo-electron microscopy structures of the Escherichia coli RNA polymerase (RNAP) σ70 holoenzyme during rRNA promoter recognition with and without DksA/ppGpp. RNAP contacts the UP element using dimerized α subunit carboxyl-terminal domains and scrunches the template DNA with the σ finger and β’ lid to select the transcription start site favorable for rapid promoter escape. Promoter binding induces conformational change of σ domain 2 that opens a gate for DNA loading and ejects σ1.1 from the RNAP cleft to facilitate open complex formation. DksA/ppGpp binding also opens the DNA loading gate, which is not coupled to σ1.1 ejection and impedes open complex formation. These results provide a molecular basis for the exceptionally active rRNA transcription and its vulnerability to DksA/ppGpp.

show abstract

Section: Methodsmentioning

confidence: 99%

Structural basis of ribosomal RNA transcription regulation

et al. 2021

View full text Add to dashboard Cite

show abstract

“…Following reconstruction in RELION, the final subset of 65,356 particles was subjected to 3D variability analysis in Cryosparc 45 . 3D variability analysis was performed solving for 3 conformational modes, and the results visualised in ChimeraX 64 .…”

Section: Methodsmentioning

confidence: 99%

Molecular basis for RNA polymerase-dependent transcription complex recycling by the helicase-like motor protein HelD

et al. 2020

View full text Add to dashboard Cite

In bacteria, transcription complexes stalled on DNA represent a major source of roadblocks for the DNA replication machinery that must be removed in order to prevent damaging collisions. Gram-positive bacteria contain a transcription factor HelD that is able to remove and recycle stalled complexes, but it was not known how it performed this function. Here, using single particle cryo-electron microscopy, we have determined the structures of Bacillus subtilis RNA polymerase (RNAP) elongation and HelD complexes, enabling analysis of the conformational changes that occur in RNAP driven by HelD interaction. HelD has a 2-armed structure which penetrates deep into the primary and secondary channels of RNA polymerase. One arm removes nucleic acids from the active site, and the other induces a large conformational change in the primary channel leading to removal and recycling of the stalled polymerase, representing a novel mechanism for recycling transcription complexes in bacteria.

show abstract

“…Model quality was assessed using MolProbity within Phenix 38 which revealed excellent stereochemistry for all three structural models (Extended Data Table 1). Figures were prepared with PyMol and ChimeraX 39 .…”

Section: Methodsmentioning

confidence: 99%

Mechanism of SARS-CoV-2 polymerase inhibition by remdesivir

Kokić

Hillen

Tegunov

et al. 2020

Preprint

View full text Add to dashboard Cite

Remdesivir is the only FDA-approved drug for the treatment of COVID-19 patients. The active form of remdesivir acts as a nucleoside analogue and inhibits the RNA-dependent RNA polymerase (RdRp) of coronaviruses including SARS-CoV-2. Remdesivir is incorporated by the RdRp into the growing RNA product and allows for addition of three more nucleotides before RNA synthesis stalls. Here we use synthetic RNA chemistry, biochemistry and cryo-electron microscopy to establish the molecular mechanism of remdesivir-induced RdRp stalling. We show that addition of the fourth nucleotide following remdesivir incorporation into the RNA product is impaired by a barrier to further RNA translocation. This translocation barrier causes retention of the RNA 3'-nucleotide in the substrate-binding site of the RdRp and interferes with entry of the next nucleoside triphosphate, thereby stalling RdRp. In the structure of the remdesivir-stalled state, the 3'-nucleotide of the RNA product is matched with the template base, and this may prevent proofreading by the viral 3'-exonuclease that recognizes mismatches. These mechanistic insights should facilitate the quest for improved antivirals that target coronavirus replication.

show abstract

UCSF ChimeraX: Structure visualization for researchers, educators, and developers

Cited by 5,813 publications

References 42 publications

Structural basis of ribosomal RNA transcription regulation

Structural basis of ribosomal RNA transcription regulation

Molecular basis for RNA polymerase-dependent transcription complex recycling by the helicase-like motor protein HelD

Mechanism of SARS-CoV-2 polymerase inhibition by remdesivir

Contact Info

Product

Resources

About