4A3B

RNA Polymerase II initial transcribing complex with a 4nt DNA-RNA hybrid

Summary for 4A3B

• Entry DOI: 10.2210/pdb4a3b/pdb
• Related: 1A1D 1DZF 1I3Q 1I50 1I6H 1K83 1NIK 1NT9 1PQV 1R5U 1R9S 1R9T 1SFO 1TWA 1TWC 1TWF 1TWG 1TWH 1WCM 1Y14 1Y1V 1Y1W 1Y1Y 1Y77 2B63 2B8K 2JA5 2JA6 2JA7 2JA8 2VUM 4A3C 4A3D 4A3E 4A3F 4A3G 4A3I 4A3J 4A3K 4A3L 4A3M
• Descriptor: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1, DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 5, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11, ... (17 entities in total)
• Functional Keywords: transcription, transcription initiation
• Biological source: SACCHAROMYCES CEREVISIAE (BAKER'S YEAST); More
• Total number of polymer chains: 15
• Total formula weight: 528131.27

Authors

Cheung, A.C.M.,Sainsbury, S.,Cramer, P. (deposition date: 2011-09-30, release date: 2011-12-07, Last modification date: 2024-05-08)

Primary citation

Cheung, A.C.,Sainsbury, S.,Cramer, P.
Structural basis of initial RNA polymerase II transcription.
EMBO J., 30:4755-4763, 2011

PubMed Abstract: During transcription initiation by RNA polymerase (Pol) II, a transient open promoter complex (OC) is converted to an initially transcribing complex (ITC) containing short RNAs, and to a stable elongation complex (EC). We report structures of a Pol II-DNA complex mimicking part of the OC, and of complexes representing minimal ITCs with 2, 4, 5, 6, and 7 nucleotide (nt) RNAs, with and without a non-hydrolyzable nucleoside triphosphate (NTP) in the insertion site +1. The partial OC structure reveals that Pol II positions the melted template strand opposite the active site. The ITC-mimicking structures show that two invariant lysine residues anchor the 3'-proximal phosphate of short RNAs. Short DNA-RNA hybrids adopt a tilted conformation that excludes the +1 template nt from the active site. NTP binding induces complete DNA translocation and the standard hybrid conformation. Conserved NTP contacts indicate a universal mechanism of NTP selection. The essential residue Q1078 in the closed trigger loop binds the NTP 2'-OH group, explaining how the trigger loop couples catalysis to NTP selection, suppressing dNTP binding and DNA synthesis.

PubMed: 22056778
DOI: 10.1038/emboj.2011.396

Experimental method

X-RAY DIFFRACTION (3.5 Å)