2VUM

Alpha-amanitin inhibited complete RNA polymerase II elongation complex

Summary for 2VUM

• Entry DOI: 10.2210/pdb2vum/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
• Descriptor: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1, DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC5, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11, ... (18 entities in total)
• Functional Keywords: transferase, dna-directed rna polymerase, alpha-amanitin, ubl conjugation, nuclear protein, rna polymerase ii, elongation complex, mrna processing, phosphorylation, enzyme inhibition, dna damage, dna repair, zinc-finger, dna-binding, transferase/dna/rna, transcription bubble, zinc, nucleus, cytoplasm, inhibitor, magnesium, transcription inhibition, translocation intermediate, transcription, metal-binding, phosphoprotein, intermediate, fungal toxin, polymorphism, nucleotidyltransferase, transcription mechanism
• Biological source: SACCHAROMYCES CEREVISIAE (BAKERS' YEAST); More
• Total number of polymer chains: 16
• Total formula weight: 531503.86

Authors

Brueckner, F.,Cramer, P. (deposition date: 2008-05-27, release date: 2008-06-17, Last modification date: 2023-12-13)

Primary citation

Brueckner, F.,Cramer, P.
Structural Basis of Transcription Inhibition by Alpha-Amanitin and Implications for RNA Polymerase II Translocation.
Nat.Struct.Mol.Biol., 15:811-, 2008

PubMed Abstract: To study how RNA polymerase II translocates after nucleotide incorporation, we prepared elongation complex crystals in which pre- and post-translocation states interconvert. Crystal soaking with the inhibitor alpha-amanitin locked the elongation complex in a new state, which was refined at 3.4-A resolution and identified as a possible translocation intermediate. The DNA base entering the active site occupies a 'pretemplating' position above the central bridge helix, which is shifted and occludes the templating position. A leucine residue in the trigger loop forms a wedge at the shifted bridge helix, but moves by 13 A to close the active site during nucleotide incorporation. Our results support a Brownian ratchet mechanism that involves swinging of the trigger loop between open, wedged and closed positions, and suggest that alpha-amanitin impairs nucleotide incorporation and translocation by trapping the trigger loop and bridge helix.

PubMed: 18552824
DOI: 10.1038/NSMB.1458

Experimental method

X-RAY DIFFRACTION (3.4 Å)