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	Clamp conformational flexibility and dynamics in archaeal and eukaryotic RNA polymerases revealed by cryo-EM.
Journal, issue, pages	J Biol Chem, Vol. 302, Issue 9, Page 113389, Year 2026
Publish date	Aug 4, 2026
Authors	George N R Fordjour / Leon Palao / Kenji Murakami / Jean-Paul Armache / Katsuhiko S Murakami /
PubMed Abstract	All cellular RNA polymerases (RNAPs) across Bacteria, Archaea, and Eukarya share a conserved catalytic core, yet bacterial and archaeal-eukaryotic RNAPs diverged after separation from the last ...All cellular RNA polymerases (RNAPs) across Bacteria, Archaea, and Eukarya share a conserved catalytic core, yet bacterial and archaeal-eukaryotic RNAPs diverged after separation from the last universal common ancestor. This evolutionary split produced distinct subunit compositions and fundamentally different requirements for external factors during transcription initiation. Bacterial RNAP relies on a σ factor, whereas archaeal-eukaryotic RNAPs require a more extensive set of general transcription factors (GTFs) to bind promoter DNA, unwind the duplex, and position the template strand within the active site cleft. Notably, despite the close structural similarity between archaeal and eukaryotic RNAPs, the requirement for GTFs became further specialized after the emergence of Eukarya. This divergence raises the question of whether differences in intrinsic conformational flexibility and dynamics of these RNAPs contribute to distinct promoter-loading pathways. In this study, we addressed this question using cryo-electron microscopy (cryo-EM) to examine archaeal RNAPs from Euryarchaeota and Crenarchaeota alongside yeast RNAP II. Archaeal RNAP displays a highly dynamic DNA binding clamp domain that samples a broad spectrum of open and closed states, whereas RNAP II predominantly adopts a closed clamp state. Both archaeal and eukaryotic RNAPs can be found in stalk-bound and stalk-less forms. Comparative structural analyses further reveal a unique conformational transition in crenarchaeal RNAP associated with clamp opening. Together, these findings define the intrinsic clamp-conformational landscapes across the archaeal-eukaryotic lineage and suggest that evolutionary tuning of clamp flexibility and dynamics contributes to distinct GTF-dependent promoter-loading mechanisms.
External links	J Biol Chem / PubMed:42551829 / PubMed Central
Methods	EM (single particle)
Resolution	3.31 - 8.9 Å
Structure data	74465 9zo4 EMDB-74465, PDB-9zo4: Cryo-EM structure of the complete Pyrococcus furiosus RNA polymerase in closed clamp conformation Method: EM (single particle) / Resolution: 4.05 Å 74466 9zo5 EMDB-74466, PDB-9zo5: Cryo-EM structure of the complete Pyrococcus furiosus RNA polymerase in open clamp conformation Method: EM (single particle) / Resolution: 4.05 Å 74490 9zof EMDB-74490, PDB-9zof: Cryo-EM structure of the complete Sulfolobus acidocaldarius RNA polymerase in closed clamp conformation Method: EM (single particle) / Resolution: 3.37 Å 74496 9zoh EMDB-74496, PDB-9zoh: Cryo-EM structure of the complete Sulfolobus acidocaldarius RNA polymerase in open clamp conformation Method: EM (single particle) / Resolution: 3.87 Å 74528 9zpk EMDB-74528, PDB-9zpk: Cryo-EM structure of the complete Saccharomyces cerevisiae RNA polymerase II in closed clamp conformation Method: EM (single particle) / Resolution: 3.31 Å 74529 9zpl EMDB-74529, PDB-9zpl: Cryo-EM structure of the complete Saccharomyces cerevisiae RNA polymerase II in open clamp conformation Method: EM (single particle) / Resolution: 3.75 Å 77809 36ro EMDB-77809, PDB-36ro: Cryo-EM structure of Pyrococcus furiosus RNA polymerase without stalk (no Rpo4/Rpo7) Method: EM (single particle) / Resolution: 4.56 Å 77810 36rp EMDB-77810, PDB-36rp: Cryo-EM structure of Sulfolobus acidocaldarius RNA polymerase without stalk (no Rpo4/Rpo7) Method: EM (single particle) / Resolution: 8.9 Å 77811 36rs EMDB-77811, PDB-36rs: Cryo-EM structure of Saccharomyces cerevisiae RNA polymerase II without stalk (no Rpb4/Rpb7) Method: EM (single particle) / Resolution: 6.75 Å
Chemicals	ChemComp-ZN: Unknown entry ChemComp-SF4: IRON/SULFUR CLUSTER
Source	pyrococcus furiosus dsm 3638 (archaea) sulfolobus acidocaldarius dsm 639 (acidophilic) saccharomyces cerevisiae (brewer's yeast)
Keywords	TRANSCRIPTION / RNA polymerase / Clamp conformation / Euryarchaea / Stalk / Crenarchaea / Eukaryote / Conformations / Promoter loading / RNA polymerase II