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PDBsum entry 3k7a

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Transcription PDB id
3k7a
Jmol
Contents
Protein chains
1408 a.a.
1122 a.a.
266 a.a.
214 a.a.
84 a.a.
133 a.a.
118 a.a.
65 a.a.
114 a.a.
46 a.a.
187 a.a.
Metals
_ZN ×9

References listed in PDB file
Key reference
Title Structure of an RNA polymerase ii-Tfiib complex and the transcription initiation mechanism.
Authors X.Liu, D.A.Bushnell, D.Wang, G.Calero, R.D.Kornberg.
Ref. Science, 2010, 327, 206-209. [DOI no: 10.1126/science.1182015]
PubMed id 19965383
Abstract
Previous x-ray crystal structures have given insight into the mechanism of transcription and the role of general transcription factors in the initiation of the process. A structure of an RNA polymerase II-general transcription factor TFIIB complex at 4.5 angstrom resolution revealed the amino-terminal region of TFIIB, including a loop termed the "B finger," reaching into the active center of the polymerase where it may interact with both DNA and RNA, but this structure showed little of the carboxyl-terminal region. A new crystal structure of the same complex at 3.8 angstrom resolution obtained under different solution conditions is complementary with the previous one, revealing the carboxyl-terminal region of TFIIB, located above the polymerase active center cleft, but showing none of the B finger. In the new structure, the linker between the amino- and carboxyl-terminal regions can also be seen, snaking down from above the cleft toward the active center. The two structures, taken together with others previously obtained, dispel long-standing mysteries of the transcription initiation process.
Figure 1.
Structure of pol II TFIIB complex. (A) "Top" view of pol II in a surface representation, with previously identified domains in the colors indicated, and with TFIIB in ribbon representation. TFIIB zinc ribbon (TFIIB[N]), linker (TFIIB[L]), first cyclin repeat (TFIIB[C]) are indicated. (B) Difference (F[o]-F[c]) electron density map between pol II TFIIB and pol II alone, contoured at 2.0[sigma], shown in green mesh, and Se-Met anomalous peaks, contoured at 6-10[sigma], shown in blue mesh. Science. Author manuscript; available in PMC 2010 January 28. Published in final edited form as: Science. 2010 January 8; 327(5962): 206. Published online 2009 November 12. doi: 10.1126/science.1182015. Copyright notice and Disclaimer
Figure 3.
Comparison of TFIIB and bacterial [sigma] factor structures. (A) Superposition of TFIIB (red) and [sigma] factor (green) structures. Conserved residues H455 and E458 of [sigma] factors that bind to the -10 element and mark the start of transcription bubble formation are highlighted as blue spheres. Corresponding domains from TFIIB and [sigma] factor are labeled. (B) Same as (A) rotated 45[deg] around the X-axis. The B-finger (TFIIB[F]) from the previous cocrystal structure is shown as a dashed black line. Science. Author manuscript; available in PMC 2010 January 28. Published in final edited form as: Science. 2010 January 8; 327(5962): 206. Published online 2009 November 12. doi: 10.1126/science.1182015. Copyright notice and Disclaimer
The above figures are reprinted from an Open Access publication published by the AAAs: Science (2010, 327, 206-209) copyright 2010.
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