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==Three-dimensional EM structure of an intact activator-dependent transcription initiation complex==
==Three-dimensional EM structure of an intact activator-dependent transcription initiation complex==
<StructureSection load='3iyd' size='340' side='right' caption='[[3iyd]], [[Resolution|resolution]] 19.80&Aring;' scene=''>
<SX load='3iyd' size='340' side='right' viewer='molstar' caption='[[3iyd]], [[Resolution|resolution]] 19.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3iyd]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IYD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IYD FirstGlance]. <br>
<table><tr><td colspan='2'>[[3iyd]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IYD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IYD FirstGlance]. <br>
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CMP:ADENOSINE-3,5-CYCLIC-MONOPHOSPHATE'>CMP</scene><br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 19.8&#8491;</td></tr>
<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">b3295, JW3257, pez, phs, rpoA, RpoB, RpoC, RpoD, RpoZ, sez ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]), rpoB, groN, nitB, rif, ron, stl, stv, tabD, b3987, JW3950 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]), rpoZ, b3649, JW3624 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 Escherichia coli K-12]), rpoD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 Escherichia coli K-12]), crp, cap, csm, b3357, JW5702 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 Escherichia coli K-12])</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CMP:ADENOSINE-3,5-CYCLIC-MONOPHOSPHATE'>CMP</scene></td></tr>
<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_RNA_polymerase DNA-directed RNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.6 2.7.7.6] </span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3iyd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iyd OCA], [https://pdbe.org/3iyd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3iyd RCSB], [https://www.ebi.ac.uk/pdbsum/3iyd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3iyd ProSAT]</span></td></tr>
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3iyd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iyd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3iyd RCSB], [http://www.ebi.ac.uk/pdbsum/3iyd PDBsum]</span></td></tr>
</table>
<table>
== Function ==
[https://www.uniprot.org/uniprot/RPOA_ECOLI RPOA_ECOLI] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. This subunit plays an important role in subunit assembly since its dimerization is the first step in the sequential assembly of subunits to form the holoenzyme.[HAMAP-Rule:MF_00059]
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
Check<jmol>
   <jmolCheckbox>
   <jmolCheckbox>
     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/iy/3iyd_consurf.spt"</scriptWhenChecked>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/iy/3iyd_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
   </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3iyd ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
We present the experimentally determined 3D structure of an intact activator-dependent transcription initiation complex comprising the Escherichia coli catabolite activator protein (CAP), RNA polymerase holoenzyme (RNAP), and a DNA fragment containing positions -78 to +20 of a Class I CAP-dependent promoter with a CAP site at position -61.5 and a premelted transcription bubble. A 20-A electron microscopy reconstruction was obtained by iterative projection-based matching of single particles visualized in carbon-sandwich negative stain and was fitted using atomic coordinate sets for CAP, RNAP, and DNA. The structure defines the organization of a Class I CAP-RNAP-promoter complex and supports previously proposed interactions of CAP with RNAP alpha subunit C-terminal domain (alphaCTD), interactions of alphaCTD with sigma(70) region 4, interactions of CAP and RNAP with promoter DNA, and phased-DNA-bend-dependent partial wrapping of DNA around the complex. The structure also reveals the positions and shapes of species-specific domains within the RNAP beta', beta, and sigma(70) subunits.
Three-dimensional EM structure of an intact activator-dependent transcription initiation complex.,Hudson BP, Quispe J, Lara-Gonzalez S, Kim Y, Berman HM, Arnold E, Ebright RH, Lawson CL Proc Natl Acad Sci U S A. 2009 Nov 24;106(47):19830-5. Epub 2009 Nov 10. PMID:19903881<ref>PMID:19903881</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>


==See Also==
==See Also==
*[[Catabolite gene activator protein|Catabolite gene activator protein]]
*[[Catabolite gene activator protein 3D structures|Catabolite gene activator protein 3D structures]]
*[[RNA polymerase|RNA polymerase]]
*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
*[[Sigma factor|Sigma factor]]
*[[Sigma factor 3D structures|Sigma factor 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</SX>
[[Category: DNA-directed RNA polymerase]]
[[Category: Escherichia coli K-12]]
[[Category: Escherichia coli]]
[[Category: Large Structures]]
[[Category: Escherichia coli k-12]]
[[Category: Arnold E]]
[[Category: Arnold, E.]]
[[Category: Berman H]]
[[Category: Berman, H.]]
[[Category: Ebright RH]]
[[Category: Ebright, R H.]]
[[Category: Hudson BP]]
[[Category: Hudson, B P.]]
[[Category: Kim Y]]
[[Category: Kim, Y.]]
[[Category: Lara S]]
[[Category: Lara, S.]]
[[Category: Lawson CL]]
[[Category: Lawson, C L.]]
[[Category: Quispe J]]
[[Category: Quispe, J.]]
[[Category: Activator]]
[[Category: Camp]]
[[Category: Camp-binding]]
[[Category: Camp-dependent]]
[[Category: Cap]]
[[Category: Class i]]
[[Category: Crp]]
[[Category: Dna]]
[[Category: Dna-binding]]
[[Category: Dna-directed rna polymerase]]
[[Category: Holoenzyme]]
[[Category: Initiation]]
[[Category: Nucleotide-binding]]
[[Category: Nucleotidyltransferase]]
[[Category: Open complex]]
[[Category: Prokaryotic]]
[[Category: Rna polymerase]]
[[Category: Sigma factor]]
[[Category: Sigma70]]
[[Category: Transcription]]
[[Category: Transcription regulation]]
[[Category: Transcription-dna complex]]
[[Category: Transferase]]
Retrieved from "https://proteopedia.org/3iyd"