Transcription initiation factor
From Proteopedia
(Difference between revisions)
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* '''TFIIA''' is one of several TFs which are required for transcription. TFIIA aids in binding the TATA-binding protein (TBP) to the TATA box containing sequence of the DNA.<br /> | * '''TFIIA''' is one of several TFs which are required for transcription. TFIIA aids in binding the TATA-binding protein (TBP) to the TATA box containing sequence of the DNA.<br /> | ||
* '''TFIIB''' bridges between TFIID and RNA polymerase II<ref>PMID:1876184</ref>.<br /> | * '''TFIIB''' bridges between TFIID and RNA polymerase II<ref>PMID:1876184</ref>.<br /> | ||
| + | * '''TFIIIB''' is the core RNA polymerase III initiation factor. It recruits pol III to the transcriptional start site<ref>PMID:17073756</ref>.<br /> | ||
* '''TFIID''' recognizes the promoter sequence on the DNA.<br /> | * '''TFIID''' recognizes the promoter sequence on the DNA.<br /> | ||
* '''TFIIE''' both subunits are are essential to form a preinitiation complex.<ref>PMID:1956398</ref><br /> | * '''TFIIE''' both subunits are are essential to form a preinitiation complex.<ref>PMID:1956398</ref><br /> | ||
* '''TFIIF''' binds RNA polymerase III prohibiting it to bind to DNA outside the promoter.<br /> | * '''TFIIF''' binds RNA polymerase III prohibiting it to bind to DNA outside the promoter.<br /> | ||
| - | * '''TF | + | * '''TF RRN''' initiate transcription by RNA polymerase I in yeast.<ref>PMID:8670901</ref><br /> |
<scene name='51/517377/Cv/3'>Human TFIIB complex with TATA-binding protein and DNA</scene> (PDB entry [[1vol]]). | <scene name='51/517377/Cv/3'>Human TFIIB complex with TATA-binding protein and DNA</scene> (PDB entry [[1vol]]). | ||
| + | ==3D structures of transcription initiation factors== | ||
| + | [[Transcription initiation factors 3D structures]] | ||
| + | |||
</StructureSection> | </StructureSection> | ||
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*TFIIA | *TFIIA | ||
| + | **[[5m4s]] – hTFIIA – human<br /> | ||
| + | **[[6mzm]] – hTFIIA+TFIID + TBP + DNA – Cryo EM<br /> | ||
| + | **[[1nvp]] – hTFIIA + TBP + DNA <br /> | ||
| + | **[[5fur]] – hTFIIA + hTFIIF + TBP + DNA - CryoEM<br /> | ||
**[[1ytf]], [[1nh2]], [[1rm1]] – yTFIIA + TBP + DNA – yeast<br /> | **[[1ytf]], [[1nh2]], [[1rm1]] – yTFIIA + TBP + DNA – yeast<br /> | ||
| - | **[[5m4s]] – hTFIIA – human<br /> | ||
| - | **[[1nvp]] – hTFIIA + TATA-binding protein + DNA <br /> | ||
| - | **[[5fur]] – hTFIIA + hTFIIF + TATA-binding protein + DNA - CryoEM<br /> | ||
*TFIIB | *TFIIB | ||
| - | **[[1pft]] – TFIIB N terminal – ''Pyrococcus furiosus'' – NMR<BR /> | ||
**[[1tfb]] – hTFIIB - NMR<BR /> | **[[1tfb]] – hTFIIB - NMR<BR /> | ||
**[[1dl6]] - hTFIIB N terminal – NMR<br /> | **[[1dl6]] - hTFIIB N terminal – NMR<br /> | ||
| + | **[[5wh1]] - hTFIIB C terminal <br /> | ||
**[[1rly]] - hTFIIB Zn ribbon domain + Zn – NMR<br /> | **[[1rly]] - hTFIIB Zn ribbon domain + Zn – NMR<br /> | ||
**[[1ro4]] - hTFIIB Zn ribbon domain – NMR<br /> | **[[1ro4]] - hTFIIB Zn ribbon domain – NMR<br /> | ||
| - | **[[1ais]], [[1d3u]] - TFIIB C terminal + TBP + DNA – ''Pyrococcus woesei'' | + | **[[1ais]], [[1d3u]] - TFIIB C terminal + TBP + DNA – ''Pyrococcus woesei''<br /> |
| + | **[[1pft]] – TFIIB N terminal – ''Pyrococcus furiosus'' – NMR<BR /> | ||
| + | **[[5o9j]], [[5o9i]] - TFIIB – ''Methanocaldococcus jannaschii'' <br /> | ||
| + | |||
| + | *TFIIA+TFIIB | ||
| + | |||
| + | **[[6o9l]] – hTFIIA+TFIIB in RNA polymerase II – Cryo EM<br /> | ||
| + | |||
| + | *TFIIIB | ||
| + | |||
| + | **[[5n9g]] – hTFIIIB + TBP + DNA<br /> | ||
| + | **[[6f44]], [[6f42]], [[6f41]], [[6f40]], [[6eu0]], [[6cnf]], [[6cnd]], [[6cnc]], [[6cnb]] – yTFIIIB + RNA polymerase III – Cryo EM<br /> | ||
*TFIID | *TFIID | ||
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**[[1bh8]] – hTFIID<BR /> | **[[1bh8]] – hTFIID<BR /> | ||
**[[1eqf]] – hTFIID subunit 1<br /> | **[[1eqf]] – hTFIID subunit 1<br /> | ||
| + | **[[6fic]] – hTFIID subunit 1 + inhibitor<br /> | ||
**[[3uv5]] – hTFIID subunit 1 bromodomain 1-2<br /> | **[[3uv5]] – hTFIID subunit 1 bromodomain 1-2<br /> | ||
**[[3uv4]] – hTFIID subunit 1 bromodomain 2<br /> | **[[3uv4]] – hTFIID subunit 1 bromodomain 2<br /> | ||
| + | **[[6bqd]] – hTFIID subunit 1 bromodomain 2 + inhibitor <br /> | ||
**[[3aad]] – hTFIID subunit 1 bromodomain 1-2 + histone chaperone ASF1A<br /> | **[[3aad]] – hTFIID subunit 1 bromodomain 1-2 + histone chaperone ASF1A<br /> | ||
**[[5mg2]] – hTFIID subunit 1 bromodomain 2 + inhibitor<br /> | **[[5mg2]] – hTFIID subunit 1 bromodomain 2 + inhibitor<br /> | ||
**[[4yym]], [[4yyn]] – hTFIID subunit 1 bromodomain 2 + histone peptide<br /> | **[[4yym]], [[4yyn]] – hTFIID subunit 1 bromodomain 2 + histone peptide<br /> | ||
| - | **[[5c13]], [[5wxg]] – hTFIID subunit 3 + histone peptide<br /> | + | **[[5c13]], [[5wxg]], [[5mxy]] – hTFIID subunit 3 PHD finger + histone peptide<br /> |
**[[5wxh]] – hTFIID subunit 3 PHD finger + histone peptide<br /> | **[[5wxh]] – hTFIID subunit 3 PHD finger + histone peptide<br /> | ||
**[[5i1q]], [[5i29]] – hTFIID subunit 1 bromodomain 2 + pyrrolopyridone<br /> | **[[5i1q]], [[5i29]] – hTFIID subunit 1 bromodomain 2 + pyrrolopyridone<br /> | ||
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**[[4wv4]] - hTFIID subunits 8+10 <br /> | **[[4wv4]] - hTFIID subunits 8+10 <br /> | ||
**[[4grw]] - hTFIID subunits 1+7 <br /> | **[[4grw]] - hTFIID subunits 1+7 <br /> | ||
| - | **[[ | + | **[[6f39]] - hTFIID subunits 5+6+9 <br /> |
| - | **[[ | + | **[[6mzl]] - hTFIID subunits 1-13 + TBP – Cryo EM<br /> |
| - | **[[ | + | **[[6mzd]] - hTFIID subunits 1,3-6,9-13 + TBP – Cryo EM<br /> |
| + | **[[6mzc]] - hTFIID subunits 2,4-6,8-12 – Cryo EM<br /> | ||
**[[1bh9]] – hTFIID + PCMBS<BR /> | **[[1bh9]] – hTFIID + PCMBS<BR /> | ||
| - | **[[1qn3]], [[1qn4]], [[1qn5]], [[1qn6]], [[1qn7]], [[1qn8]], [[1qn9]], [[1qna]], [[1qnb]], [[1qnc]], [[1qne]] – TFIID + DNA – ''Arabidopsis thaliana'' | + | **[[6df7]], [[6df4]] – TFIID subunit 1 bromodomain 2 + inhibitor - rabbit<br /> |
| + | **[[1tba]] – TFIID – ''Drosophila melanogaster'' - NMR<BR /> | ||
| + | **[[1qn3]], [[1qn4]], [[1qn5]], [[1qn6]], [[1qn7]], [[1qn8]], [[1qn9]], [[1qna]], [[1qnb]], [[1qnc]], [[1qne]] – TFIID + DNA – ''Arabidopsis thaliana''<br /> | ||
| + | **[[4oy2]] - yTFIID subunits 1+7 <br /> | ||
| + | **[[6mip]] - yTFIID subunits 14 <br /> | ||
| + | **[[5iok]], [[5o7e]], [[6miq]], [[6mio]], [[6min]] – yTFIID subunit 14 + histone peptide<br /> | ||
| + | **[[6t9j]] - yTFIID subunit 12 + Spt20 + transcription-associated protein – Cryo EM <br /> | ||
| + | **[[6t9k]], [[6t9i]] - yTFIID in SAGA complex – Cryo EM <br /> | ||
| + | **[[6tbm]], [[6tb4]] - TFIID in SAGA complex – ''Komagataella phaffii'' – Cryo EM <br /> | ||
*TFIIE | *TFIIE | ||
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*TF in RNA polymerase II | *TF in RNA polymerase II | ||
| + | **[[5iy6]], [[5iy7]], [[5iy8]], [[5iy9]], [[5iya]], [[5iyb]], [[5iyc]], [[5iyd]] – hTFIIA + hTFIIB + hTFIIE + hTFIIF + hTFIIH + DNA – Cryo EM<br /> | ||
**[[5fyw]] – yTFIIA + yTFIIE + yTFIIF + DNA <br /> | **[[5fyw]] – yTFIIA + yTFIIE + yTFIIF + DNA <br /> | ||
| - | **[[5fz5]] – yTFIIA + yTFIIE + yTFIIF + DNA – Cryo EM<br /> | + | **[[5fz5]], [[6gym]], [[6gyl]] – yTFIIA + yTFIIE + yTFIIF + DNA – Cryo EM<br /> |
| + | **[[6gyk]] – yTFIIA + yTFIIB + yTFIIF + DNA – Cryo EM<br /> | ||
**[[4v1o]], [[4v1n]] – yTFIIB + yTFIIF – Cryo EM<br /> | **[[4v1o]], [[4v1n]] – yTFIIB + yTFIIF – Cryo EM<br /> | ||
**[[3k1f]], [[3k7a]], [[4bbr]], [[4bbs]] – yTFIIB <br /> | **[[3k1f]], [[3k7a]], [[4bbr]], [[4bbs]] – yTFIIB <br /> | ||
| - | **[[5iy6]], [[5iy7]], [[5iy8]], [[5iy9]], [[5iya]], [[5iyb]], [[5iyc]], [[5iyd]] – hTFIIA + hTFIIB + hTFIIE + hTFIIF + hTFIIH + DNA – Cryo EM<br /> | ||
**[[5fmf]], [[5sva]], [[5oqj]], [[5oqm]] – yTFIIA + yTFIIB + yTFIIE + yTFIIF + yTFIIH + DNA – Cryo EM<br /> | **[[5fmf]], [[5sva]], [[5oqj]], [[5oqm]] – yTFIIA + yTFIIB + yTFIIE + yTFIIF + yTFIIH + DNA – Cryo EM<br /> | ||
| - | *TF | + | *TF RRN in RNA polymerase I |
| + | **[[5o7x]] – yTF RRN6+RRN7+RRN11 <br /> | ||
**[[5g5l]] – yTF RRN3 in RNA polymerase I<br /> | **[[5g5l]] – yTF RRN3 in RNA polymerase I<br /> | ||
| + | **[[6rrd]], [[6rqt]] – yTF RRN3 in RNA polymerase I – Cryo EM<br /> | ||
| + | **[[6ruo]] – yTF RRN3+RRN6+RRN11 in RNA polymerase I – Cryo EM<br /> | ||
| + | **[[5w66]], [[5w65]], [[5w64]], [[5w5y]], [[5oa1]] – yTF RRN6+RRN7+RRN11 in RNA polymerase I – Cryo EM<br /> | ||
| + | **[[6rwe]], [[6rui]], [[6rql]], [[6rqh]], [[5n61]], [[5n60]], [[5n5z]], [[5n5y]] – yTF RRN3+RRN6+RRN7+RRN11 in RNA polymerase I – Cryo EM<br /> | ||
Revision as of 08:50, 4 March 2020
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3D structures of transcription initiation factors
Updated on 04-March-2020
References
- ↑ Roeder RG. The role of general initiation factors in transcription by RNA polymerase II. Trends Biochem Sci. 1996 Sep;21(9):327-35. PMID:8870495
- ↑ Kuhlman TC, Cho H, Reinberg D, Hernandez N. The general transcription factors IIA, IIB, IIF, and IIE are required for RNA polymerase II transcription from the human U1 small nuclear RNA promoter. Mol Cell Biol. 1999 Mar;19(3):2130-41. PMID:10022900
- ↑ Ha I, Lane WS, Reinberg D. Cloning of a human gene encoding the general transcription initiation factor IIB. Nature. 1991 Aug 22;352(6337):689-95. PMID:1876184 doi:http://dx.doi.org/10.1038/352689a0
- ↑ Kassavetis GA, Geiduschek EP. Transcription factor TFIIIB and transcription by RNA polymerase III. Biochem Soc Trans. 2006 Dec;34(Pt 6):1082-7. doi: 10.1042/BST0341082. PMID:17073756 doi:http://dx.doi.org/10.1042/BST0341082
- ↑ Peterson MG, Inostroza J, Maxon ME, Flores O, Admon A, Reinberg D, Tjian R. Structure and functional properties of human general transcription factor IIE. Nature. 1991 Dec 5;354(6352):369-73. PMID:1956398 doi:http://dx.doi.org/10.1038/354369a0
- ↑ Yamamoto RT, Nogi Y, Dodd JA, Nomura M. RRN3 gene of Saccharomyces cerevisiae encodes an essential RNA polymerase I transcription factor which interacts with the polymerase independently of DNA template. EMBO J. 1996 Aug 1;15(15):3964-73. PMID:8670901
