6KF4

Cryo-EM structure of Thermococcus kodakarensis RNA polymerase

Summary for 6KF4

• Entry DOI: 10.2210/pdb6kf4/pdb
• EMDB information: 9961 9969
• Descriptor: DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit N, DNA-directed RNA polymerase subunit P, ... (14 entities in total)
• Functional Keywords: apo-rna polymerase, transcription
• Biological source: Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1); More
• Total number of polymer chains: 12
• Total formula weight: 402559.95

Authors

Jun, S.-H.,Hyun, J.,Jeong, H.,Cha, J.S.,Kim, H.,Bartlett, M.S.,Cho, H.-S.,Murakami, K.S. (deposition date: 2019-07-06, release date: 2020-07-01, Last modification date: 2024-05-29)

Primary citation

Jun, S.H.,Hyun, J.,Cha, J.S.,Kim, H.,Bartlett, M.S.,Cho, H.S.,Murakami, K.S.
Direct binding of TFE alpha opens DNA binding cleft of RNA polymerase.
Nat Commun, 11:6123-6123, 2020

PubMed Abstract: Opening of the DNA binding cleft of cellular RNA polymerase (RNAP) is necessary for transcription initiation but the underlying molecular mechanism is not known. Here, we report on the cryo-electron microscopy structures of the RNAP, RNAP-TFEα binary, and RNAP-TFEα-promoter DNA ternary complexes from archaea, Thermococcus kodakarensis (Tko). The structures reveal that TFEα bridges the RNAP clamp and stalk domains to open the DNA binding cleft. Positioning of promoter DNA into the cleft closes it while maintaining the TFEα interactions with the RNAP mobile modules. The structures and photo-crosslinking results also suggest that the conserved aromatic residue in the extended winged-helix domain of TFEα interacts with promoter DNA to stabilize the transcription bubble. This study provides a structural basis for the functions of TFEα and elucidates the mechanism by which the DNA binding cleft is opened during transcription initiation in the stalk-containing RNAPs, including archaeal and eukaryotic RNAPs.

PubMed: 33257704
DOI: 10.1038/s41467-020-19998-x

Experimental method

ELECTRON MICROSCOPY (3.97 Å)