3j0k

From Proteopedia

(Difference between revisions)

Current revision

Orientation of RNA polymerase II within the human VP16-Mediator-pol II-TFIIF assembly

3j0k, resolution 36.00Å

Structural highlights

3j0k is a 10 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 36Å
Ligands:
Experimental data:	Check to display Experimental Data
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RPB7_YEAST DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB7 is part of a subcomplex with RPB4 that binds to a pocket formed by RPB1, RPB2 and RPB6 at the base of the clamp element. The RBP4-RPB7 subcomplex seems to lock the clamp via RPB7 in the closed conformation thus preventing double stranded DNA to enter the active site cleft. The RPB4-RPB7 subcomplex binds single-stranded DNA and RNA. The RPB4-RPB7 subcomplex recruits FCP1 to Pol II.^[1] ^[2] ^[3]

Publication Abstract from PubMed

The macromolecular assembly required to initiate transcription of protein-coding genes, known as the Pre-Initiation Complex (PIC), consists of multiple protein complexes and is approximately 3.5 MDa in size. At the heart of this assembly is the Mediator complex, which helps regulate PIC activity and interacts with the RNA polymerase II (pol II) enzyme. The structure of the human Mediator-pol II interface is not well-characterized, whereas attempts to structurally define the Mediator-pol II interaction in yeast have relied on incomplete assemblies of Mediator and/or pol II and have yielded inconsistent interpretations. We have assembled the complete, 1.9 MDa human Mediator-pol II-TFIIF complex from purified components and have characterized its structural organization using cryo-electron microscopy and single-particle reconstruction techniques. The orientation of pol II within this assembly was determined by crystal structure docking and further validated with projection matching experiments, allowing the structural organization of the entire human PIC to be envisioned. Significantly, pol II orientation within the Mediator-pol II-TFIIF assembly can be reconciled with past studies that determined the location of other PIC components relative to pol II itself. Pol II surfaces required for interacting with TFIIB, TFIIE, and promoter DNA (i.e., the pol II cleft) are exposed within the Mediator-pol II-TFIIF structure; RNA exit is unhindered along the RPB4/7 subunits; upstream and downstream DNA is accessible for binding additional factors; and no major structural re-organization is necessary to accommodate the large, multi-subunit TFIIH or TFIID complexes. The data also reveal how pol II binding excludes Mediator-CDK8 subcomplex interactions and provide a structural basis for Mediator-dependent control of PIC assembly and function. Finally, parallel structural analysis of Mediator-pol II complexes lacking TFIIF reveal that TFIIF plays a key role in stabilizing pol II orientation within the assembly.

Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly.,Bernecky C, Grob P, Ebmeier CC, Nogales E, Taatjes DJ PLoS Biol. 2011 Mar;9(3):e1000603. Epub 2011 Mar 29. PMID:21468301^[4]

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

References

↑ Orlicky SM, Tran PT, Sayre MH, Edwards AM. Dissociable Rpb4-Rpb7 subassembly of rna polymerase II binds to single-strand nucleic acid and mediates a post-recruitment step in transcription initiation. J Biol Chem. 2001 Mar 30;276(13):10097-102. Epub 2000 Nov 21. PMID:11087726 doi:10.1074/jbc.M003165200
↑ Kamenski T, Heilmeier S, Meinhart A, Cramer P. Structure and mechanism of RNA polymerase II CTD phosphatases. Mol Cell. 2004 Aug 13;15(3):399-407. PMID:15304220 doi:http://dx.doi.org/10.1016/j.molcel.2004.06.035
↑ Lotan R, Goler-Baron V, Duek L, Haimovich G, Choder M. The Rpb7p subunit of yeast RNA polymerase II plays roles in the two major cytoplasmic mRNA decay mechanisms. J Cell Biol. 2007 Sep 24;178(7):1133-43. Epub 2007 Sep 17. PMID:17875743 doi:10.1083/jcb.200701165
↑ Bernecky C, Grob P, Ebmeier CC, Nogales E, Taatjes DJ. Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly. PLoS Biol. 2011 Mar;9(3):e1000603. Epub 2011 Mar 29. PMID:21468301 doi:10.1371/journal.pbio.1000603

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/3j0k"

@@ Line 1: / Line 1: @@
-[[Image:3j0k.png|left|200px]]
-<!--
+==Orientation of RNA polymerase II within the human VP16-Mediator-pol II-TFIIF assembly==
-The line below this paragraph, containing "STRUCTURE_3j0k", creates the "Structure Box" on the page.
+<SX load='3j0k' size='340' side='right' viewer='molstar' caption='[[3j0k]], [[Resolution|resolution]] 36.00&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'>[[3j0k]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J0K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3J0K 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">Electron Microscopy, [[Resolution|Resolution]] 36&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_3j0k|  PDB=3j0k  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3j0k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j0k OCA], [https://pdbe.org/3j0k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3j0k RCSB], [https://www.ebi.ac.uk/pdbsum/3j0k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3j0k ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RPB7_YEAST RPB7_YEAST] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB7 is part of a subcomplex with RPB4 that binds to a pocket formed by RPB1, RPB2 and RPB6 at the base of the clamp element. The RBP4-RPB7 subcomplex seems to lock the clamp via RPB7 in the closed conformation thus preventing double stranded DNA to enter the active site cleft. The RPB4-RPB7 subcomplex binds single-stranded DNA and RNA. The RPB4-RPB7 subcomplex recruits FCP1 to Pol II.<ref>PMID:11087726</ref> <ref>PMID:15304220</ref> <ref>PMID:17875743</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The macromolecular assembly required to initiate transcription of protein-coding genes, known as the Pre-Initiation Complex (PIC), consists of multiple protein complexes and is approximately 3.5 MDa in size. At the heart of this assembly is the Mediator complex, which helps regulate PIC activity and interacts with the RNA polymerase II (pol II) enzyme. The structure of the human Mediator-pol II interface is not well-characterized, whereas attempts to structurally define the Mediator-pol II interaction in yeast have relied on incomplete assemblies of Mediator and/or pol II and have yielded inconsistent interpretations. We have assembled the complete, 1.9 MDa human Mediator-pol II-TFIIF complex from purified components and have characterized its structural organization using cryo-electron microscopy and single-particle reconstruction techniques. The orientation of pol II within this assembly was determined by crystal structure docking and further validated with projection matching experiments, allowing the structural organization of the entire human PIC to be envisioned. Significantly, pol II orientation within the Mediator-pol II-TFIIF assembly can be reconciled with past studies that determined the location of other PIC components relative to pol II itself. Pol II surfaces required for interacting with TFIIB, TFIIE, and promoter DNA (i.e., the pol II cleft) are exposed within the Mediator-pol II-TFIIF structure; RNA exit is unhindered along the RPB4/7 subunits; upstream and downstream DNA is accessible for binding additional factors; and no major structural re-organization is necessary to accommodate the large, multi-subunit TFIIH or TFIID complexes. The data also reveal how pol II binding excludes Mediator-CDK8 subcomplex interactions and provide a structural basis for Mediator-dependent control of PIC assembly and function. Finally, parallel structural analysis of Mediator-pol II complexes lacking TFIIF reveal that TFIIF plays a key role in stabilizing pol II orientation within the assembly.
-===Orientation of RNA polymerase II within the human VP16-Mediator-pol II-TFIIF assembly===
+Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly.,Bernecky C, Grob P, Ebmeier CC, Nogales E, Taatjes DJ PLoS Biol. 2011 Mar;9(3):e1000603. Epub 2011 Mar 29. PMID:21468301<ref>PMID:21468301</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3j0k" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_21468301}}, adds the Publication Abstract to the page
+*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 21468301 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_21468301}}
+__TOC__
+</SX>
-==About this Structure==
-[[3j0k]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J0K OCA].
-==Reference==
-<ref group="xtra">PMID:021468301</ref><references group="xtra"/>
-[[Category: DNA-directed RNA polymerase]]
 [[Category: Homo sapiens]]
-[[Category: Bernecky, C.]]
+[[Category: Large Structures]]
-[[Category: Ebmeier, C C.]]
+[[Category: Bernecky C]]
-[[Category: Grob, P.]]
+[[Category: Ebmeier CC]]
-[[Category: Nogales, E.]]
+[[Category: Grob P]]
-[[Category: Taatjes, D J.]]
+[[Category: Nogales E]]
-[[Category: Transferase-transcription complex]]
+[[Category: Taatjes DJ]]

3j0k

From Proteopedia

Current revision

Orientation of RNA polymerase II within the human VP16-Mediator-pol II-TFIIF assembly

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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