3rj1

From Proteopedia

(Difference between revisions)

Current revision

Architecture of the Mediator Head module

Structural highlights

3rj1 is a 21 chain structure with sequence from Saccharomyces cerevisiae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 4.3Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

MED17_YEAST Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. The Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins.^[1] ^[2] ^[3] ^[4] ^[5]

Publication Abstract from PubMed

Mediator is a key regulator of eukaryotic transcription, connecting activators and repressors bound to regulatory DNA elements with RNA polymerase II (Pol II). In the yeast Saccharomyces cerevisiae, Mediator comprises 25 subunits with a total mass of more than one megadalton (refs 5, 6) and is organized into three modules, called head, middle/arm and tail. Our understanding of Mediator assembly and its role in regulating transcription has been impeded so far by limited structural information. Here we report the crystal structure of the essential Mediator head module (seven subunits, with a mass of 223 kilodaltons) at a resolution of 4.3 angstroms. Our structure reveals three distinct domains, with the integrity of the complex centred on a bundle of ten helices from five different head subunits. An intricate pattern of interactions within this helical bundle ensures the stable assembly of the head subunits and provides the binding sites for general transcription factors and Pol II. Our structural and functional data suggest that the head module juxtaposes transcription factor IIH and the carboxy-terminal domain of the largest subunit of Pol II, thereby facilitating phosphorylation of the carboxy-terminal domain of Pol II. Our results reveal architectural principles underlying the role of Mediator in the regulation of gene expression.

Architecture of the Mediator head module.,Imasaki T, Calero G, Cai G, Tsai KL, Yamada K, Cardelli F, Erdjument-Bromage H, Tempst P, Berger I, Kornberg GL, Asturias FJ, Kornberg RD, Takagi Y Nature. 2011 Jul 3;475(7355):240-3. doi: 10.1038/nature10162. PMID:21725323^[6]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Kang JS, Kim SH, Hwang MS, Han SJ, Lee YC, Kim YJ. The structural and functional organization of the yeast mediator complex. J Biol Chem. 2001 Nov 9;276(45):42003-10. Epub 2001 Sep 12. PMID:11555651 doi:http://dx.doi.org/10.1074/jbc.M105961200
↑ Nair D, Kim Y, Myers LC. Mediator and TFIIH govern carboxyl-terminal domain-dependent transcription in yeast extracts. J Biol Chem. 2005 Oct 7;280(40):33739-48. Epub 2005 Aug 2. PMID:16076843 doi:http://dx.doi.org/M506067200
↑ Takagi Y, Kornberg RD. Mediator as a general transcription factor. J Biol Chem. 2006 Jan 6;281(1):80-9. Epub 2005 Nov 1. PMID:16263706 doi:http://dx.doi.org/M508253200
↑ Takagi Y, Calero G, Komori H, Brown JA, Ehrensberger AH, Hudmon A, Asturias F, Kornberg RD. Head module control of mediator interactions. Mol Cell. 2006 Aug 4;23(3):355-64. PMID:16885025 doi:http://dx.doi.org/S1097-2765(06)00412-6
↑ Holstege FC, Jennings EG, Wyrick JJ, Lee TI, Hengartner CJ, Green MR, Golub TR, Lander ES, Young RA. Dissecting the regulatory circuitry of a eukaryotic genome. Cell. 1998 Nov 25;95(5):717-28. PMID:9845373
↑ Imasaki T, Calero G, Cai G, Tsai KL, Yamada K, Cardelli F, Erdjument-Bromage H, Tempst P, Berger I, Kornberg GL, Asturias FJ, Kornberg RD, Takagi Y. Architecture of the Mediator head module. Nature. 2011 Jul 3;475(7355):240-3. doi: 10.1038/nature10162. PMID:21725323 doi:10.1038/nature10162

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3rj1"

@@ Line 1: / Line 1: @@
-[[Image:3rj1.jpg|left|200px]]
-<!--
+==Architecture of the Mediator Head module==
-The line below this paragraph, containing "STRUCTURE_3rj1", creates the "Structure Box" on the page.
+<StructureSection load='3rj1' size='340' side='right'caption='[[3rj1]], [[Resolution|resolution]] 4.30&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3rj1]] is a 21 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RJ1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RJ1 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 4.3&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SE:SELENIUM+ATOM'>SE</scene></td></tr>
-{{STRUCTURE_3rj1|  PDB=3rj1  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3rj1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rj1 OCA], [https://pdbe.org/3rj1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rj1 RCSB], [https://www.ebi.ac.uk/pdbsum/3rj1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rj1 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/MED17_YEAST MED17_YEAST] Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. The Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins.<ref>PMID:11555651</ref> <ref>PMID:16076843</ref> <ref>PMID:16263706</ref> <ref>PMID:16885025</ref> <ref>PMID:9845373</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Mediator is a key regulator of eukaryotic transcription, connecting activators and repressors bound to regulatory DNA elements with RNA polymerase II (Pol II). In the yeast Saccharomyces cerevisiae, Mediator comprises 25 subunits with a total mass of more than one megadalton (refs 5, 6) and is organized into three modules, called head, middle/arm and tail. Our understanding of Mediator assembly and its role in regulating transcription has been impeded so far by limited structural information. Here we report the crystal structure of the essential Mediator head module (seven subunits, with a mass of 223 kilodaltons) at a resolution of 4.3 angstroms. Our structure reveals three distinct domains, with the integrity of the complex centred on a bundle of ten helices from five different head subunits. An intricate pattern of interactions within this helical bundle ensures the stable assembly of the head subunits and provides the binding sites for general transcription factors and Pol II. Our structural and functional data suggest that the head module juxtaposes transcription factor IIH and the carboxy-terminal domain of the largest subunit of Pol II, thereby facilitating phosphorylation of the carboxy-terminal domain of Pol II. Our results reveal architectural principles underlying the role of Mediator in the regulation of gene expression.
-===Architecture of the Mediator Head module===
+Architecture of the Mediator head module.,Imasaki T, Calero G, Cai G, Tsai KL, Yamada K, Cardelli F, Erdjument-Bromage H, Tempst P, Berger I, Kornberg GL, Asturias FJ, Kornberg RD, Takagi Y Nature. 2011 Jul 3;475(7355):240-3. doi: 10.1038/nature10162. PMID:21725323<ref>PMID:21725323</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3rj1" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_21725323}}, adds the Publication Abstract to the page
+*[[Mediator|Mediator]]
-(as it appears on PubMed at http://www.pubmed.gov), where 21725323 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_21725323}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-[[3rj1]] is a 21 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RJ1 OCA].
-==Reference==
-<ref group="xtra">PMID:021725323</ref><references group="xtra"/>
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Asturias, F J.]]
+[[Category: Asturias FJ]]
-[[Category: Berger, I.]]
+[[Category: Berger I]]
-[[Category: Cai, G.]]
+[[Category: Cai G]]
-[[Category: Calero, G.]]
+[[Category: Calero G]]
-[[Category: Cardelli, F.]]
+[[Category: Cardelli F]]
-[[Category: Erdjument-Bromage, H.]]
+[[Category: Erdjument-Bromage H]]
-[[Category: Imasaki, T.]]
+[[Category: Imasaki T]]
-[[Category: Kornberg, G L.]]
+[[Category: Kornberg GL]]
-[[Category: Kornberg, R D.]]
+[[Category: Kornberg RD]]
-[[Category: Takagi, Y.]]
+[[Category: Takagi Y]]
-[[Category: Tempst, P.]]
+[[Category: Tempst P]]
-[[Category: Tsai, K L.]]
+[[Category: Tsai KL]]
-[[Category: Yamada, K.]]
+[[Category: Yamada K]]
-[[Category: Head module]]
-[[Category: Helical bundle]]
-[[Category: Med]]
-[[Category: Mediator]]
-[[Category: Mediator head]]
-[[Category: Nucleus]]
-[[Category: Pol ii]]
-[[Category: Regulator]]
-[[Category: Rna polymeras ii]]
-[[Category: Rna polymerase ii]]
-[[Category: Rnap]]
-[[Category: Tbp]]
-[[Category: Transcription]]
-[[Category: Transcriptional regulation]]

3rj1

From Proteopedia

Current revision

Architecture of the Mediator Head module

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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