Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Structural basis of archaeal RNA polymerase transcription elongation and Spt4/5 recruitment.
Journal, issue, pages	Nucleic Acids Res, Vol. 52, Issue 10, Page 6017-6035, Year 2024
Publish date	Jun 10, 2024
Authors	Daniela Tarău / Felix Grünberger / Michael Pilsl / Robert Reichelt / Florian Heiß / Sabine König / Henning Urlaub / Winfried Hausner / Christoph Engel / Dina Grohmann /
PubMed Abstract	Archaeal transcription is carried out by a multi-subunit RNA polymerase (RNAP) that is highly homologous in structure and function to eukaryotic RNAP II. Among the set of basal transcription factors, ...Archaeal transcription is carried out by a multi-subunit RNA polymerase (RNAP) that is highly homologous in structure and function to eukaryotic RNAP II. Among the set of basal transcription factors, only Spt5 is found in all domains of life, but Spt5 has been shaped during evolution, which is also reflected in the heterodimerization of Spt5 with Spt4 in Archaea and Eukaryotes. To unravel the mechanistic basis of Spt4/5 function in Archaea, we performed structure-function analyses using the archaeal transcriptional machinery of Pyrococcus furiosus (Pfu). We report single-particle cryo-electron microscopy reconstructions of apo RNAP and the archaeal elongation complex (EC) in the absence and presence of Spt4/5. Surprisingly, Pfu Spt4/5 also binds the RNAP in the absence of nucleic acids in a distinct super-contracted conformation. We show that the RNAP clamp/stalk module exhibits conformational flexibility in the apo state of RNAP and that the enzyme contracts upon EC formation or Spt4/5 engagement. We furthermore identified a contact of the Spt5-NGN domain with the DNA duplex that stabilizes the upstream boundary of the transcription bubble and impacts Spt4/5 activity in vitro. This study, therefore, provides the structural basis for Spt4/5 function in archaeal transcription and reveals a potential role beyond the well-described support of elongation.
External links	Nucleic Acids Res / PubMed:38709902 / PubMed Central
Methods	EM (single particle)
Resolution	3.02 - 3.45 Å
Structure data	16809 8cro EMDB-16809, PDB-8cro: Cryo-EM structure of Pyrococcus furiosus transcription elongation complex Method: EM (single particle) / Resolution: 3.1 Å 16929 8oki EMDB-16929, PDB-8oki: Cryo-EM structure of Pyrococcus furiosus transcription elongation complex bound to Spt4/5 Method: EM (single particle) / Resolution: 3.45 Å 17130 8orq EMDB-17130, PDB-8orq: Cryo-EM structure of Pyrococcus furiosus apo form RNA polymerase open clamp conformation Method: EM (single particle) / Resolution: 3.2 Å 17366 8p2i EMDB-17366, PDB-8p2i: Cryo-EM structure of Pyrococcus furiosus apo form RNA polymerase contracted clamp conformation with Spt4/5 Method: EM (single particle) / Resolution: 3.4 Å 19033 8rbo EMDB-19033, PDB-8rbo: Cryo-EM structure of Pyrococcus furiosus apo form RNA polymerase contracted clamp conformation Method: EM (single particle) / Resolution: 3.02 Å
Chemicals	ChemComp-ZN: Unknown entry ChemComp-MG: Unknown entry
Source	pyrococcus furiosus dsm 3638 (archaea)
Keywords	TRANSCRIPTION / RNA / Polymerase / Elongation / Complex / Pyrococcus furiosus / Archaea / DNA / Elongation complex