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Crystal structure of a transcription factor IIIB core interface ternary complex

Abstract

Transcription factor IIIB (TFIIIB), consisting of the TATA-binding protein (TBP), TFIIB-related factor (Brf1) and Bdp1, is a central component in basal and regulated transcription by RNA polymerase III1,2,3,4. TFIIIB recruits its polymerase to the promoter and subsequently has an essential role in the formation of the open initiation complex. The amino-terminal half of Brf1 shares a high degree of sequence similarity with the polymerase II general transcription factor TFIIB, but it is the carboxy-terminal half of Brf1 that contributes most of its binding affinity with TBP5,6,7,8. The principal anchoring region is located between residues 435 and 545 of yeast Brf1, comprising its homology domain II. The same region also provides the primary interface for assembling Bdp1 into the TFIIIB complex9. We report here a 2.95 Å resolution crystal structure of the ternary complex containing Brf1 homology domain II, the conserved region of TBP and 19 base pairs of U6 promoter DNA. The structure reveals the core interface for assembly of TFIIIB and demonstrates how the loosely packed Brf1 domain achieves remarkable binding specificity with the convex and lateral surfaces of TBP.

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Figure 1: Ribbon style representations of the yeast Brf1–TBP–DNA ternary complex.
Figure 2: Brf1 and the yeast U6 promoter.
Figure 3: Stereo illustrations of the TBP–Brf1 interactions (left panel).
Figure 4: Cross-validation with molecular genetic analysis.

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Acknowledgements

Z.S.J. would like to thank T. Steitz for financial support. The authors would like to thank A. Berk, J. Cabral, S. Harrison, N. Hernandez, F. Li, K. Struhl and Y. Xiong for discussions; G. Olack for assistance in mass spectrum analysis; M. Wilson for help with data collection; P. Mann for assistance with protein preparation; Yale CSB core staff for advice on software-related issues; W. Henderickson, C. Ogata (NSLS beamline X4A), M. Becker, L. Berman, R. Sweet (NSLS beamline X25), A. Joachimiak and SBC staff (ANL beamline 19 ID) for help with synchrotron data acquisition; and Z. Otwinowski, W. Minor, I. Minor, C. Vonrhein and G. Murshudov for advice on programs. This work was supported in part by the Howard Hughes Medical Institute and by the National Institutes of Health (E.P.G., P.B.S. and T. Steitz).

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Correspondence to Z. Sean Juo.

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Juo, Z., Kassavetis, G., Wang, J. et al. Crystal structure of a transcription factor IIIB core interface ternary complex. Nature 422, 534–539 (2003). https://doi.org/10.1038/nature01534

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