4BBS

Structure of an initially transcribing RNA polymerase II-TFIIB complex

Summary for 4BBS

• Entry DOI: 10.2210/pdb4bbs/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 4A3B 4A3C 4A3D 4A3E 4A3F 4A3G 4A3I 4A3J 4A3K 4A3L 4A3M 4A93 4BBR
• 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, ... (18 entities in total)
• Functional Keywords: transcription
• Biological source: SACCHAROMYCES CEREVISIAE (BAKER'S YEAST); More
• Cellular location: Nucleus: P04050 P38902 P29055 P08518 P16370 P20433 P20434 P34087 P20436 P27999; Nucleus, nucleolus: P22139 P40422; Cytoplasm: P20435
• Total number of polymer chains: 16
• Total formula weight: 567506.18

Authors

Sainsbury, S.,Niesser, J.,Cramer, P. (deposition date: 2012-09-27, release date: 2012-11-14, Last modification date: 2024-05-08)

Primary citation

Sainsbury, S.,Niesser, J.,Cramer, P.
Structure and Function of the Initially Transcribing RNA Polymerase II-TFIIB Complex
Nature, 493:437-, 2013

PubMed Abstract: The general transcription factor (TF) IIB is required for RNA polymerase (Pol) II initiation and extends with its B-reader element into the Pol II active centre cleft. Low-resolution structures of the Pol II-TFIIB complex indicated how TFIIB functions in DNA recruitment, but they lacked nucleic acids and half of the B-reader, leaving other TFIIB functions enigmatic. Here we report crystal structures of the Pol II-TFIIB complex from the yeast Saccharomyces cerevisiae at 3.4 Å resolution and of an initially transcribing complex that additionally contains the DNA template and a 6-nucleotide RNA product. The structures reveal the entire B-reader and protein-nucleic acid interactions, and together with functional data lead to a more complete understanding of transcription initiation. TFIIB partially closes the polymerase cleft to position DNA and assist in its opening. The B-reader does not reach the active site but binds the DNA template strand upstream to assist in the recognition of the initiator sequence and in positioning the transcription start site. TFIIB rearranges active-site residues, induces binding of the catalytic metal ion B, and stimulates initial RNA synthesis allosterically. TFIIB then prevents the emerging DNA-RNA hybrid duplex from tilting, which would impair RNA synthesis. When the RNA grows beyond 6 nucleotides, it is separated from DNA and is directed to its exit tunnel by the B-reader loop. Once the RNA grows to 12-13 nucleotides, it clashes with TFIIB, triggering TFIIB displacement and elongation complex formation. Similar mechanisms may underlie all cellular transcription because all eukaryotic and archaeal RNA polymerases use TFIIB-like factors, and the bacterial initiation factor sigma has TFIIB-like topology and contains the loop region 3.2 that resembles the B-reader loop in location, charge and function. TFIIB and its counterparts may thus account for the two fundamental properties that distinguish RNA from DNA polymerases: primer-independent chain initiation and product separation from the template.

PubMed: 23151482
DOI: 10.1038/NATURE11715

Experimental method

X-RAY DIFFRACTION (3.6 Å)