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1rio

From Proteopedia

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(New page: 200px<br /><applet load="1rio" size="450" color="white" frame="true" align="right" spinBox="true" caption="1rio, resolution 2.30&Aring;" /> '''Structure of bacteri...)
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[[Image:1rio.gif|left|200px]]<br /><applet load="1rio" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1rio, resolution 2.30&Aring;" />
 
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'''Structure of bacteriophage lambda cI-NTD in complex with sigma-region4 of Thermus aquaticus bound to DNA'''<br />
 
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==Overview==
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==Structure of bacteriophage lambda cI-NTD in complex with sigma-region4 of Thermus aquaticus bound to DNA==
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The cI protein of bacteriophage lambda (lambdacI) activates transcription, by binding a DNA operator just upstream of the promoter and interacting, with the RNA polymerase sigma subunit domain 4 (sigma(4)). We determined, the crystal structure of the lambdacI/sigma(4)/DNA ternary complex at 2.3, A resolution. There are no conformational changes in either protein, which, interact through an extremely small interface involving at most 6 amino, acid residues. The interactions of the two proteins stabilize the binding, of each protein to the DNA. The results provide insight into how, activators can operate through a simple cooperative binding mechanism but, affect different steps of the transcription initiation process.
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<StructureSection load='1rio' size='340' side='right'caption='[[1rio]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1rio]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_Lambda Escherichia virus Lambda] and [https://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RIO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RIO FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1rio FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rio OCA], [https://pdbe.org/1rio PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rio RCSB], [https://www.ebi.ac.uk/pdbsum/1rio PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rio ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/SIGA_THEAQ SIGA_THEAQ] Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This sigma factor is the primary sigma factor during exponential growth.[HAMAP-Rule:MF_00963]<ref>PMID:11114902</ref> <ref>PMID:11931761</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ri/1rio_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1rio ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1RIO is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Enterobacteria_phage_lambda Enterobacteria phage lambda] and [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus] with CA and MPD as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1RIO OCA].
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*[[Sigma factor 3D structures|Sigma factor 3D structures]]
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== References ==
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==Reference==
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<references/>
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Structure of a ternary transcription activation complex., Jain D, Nickels BE, Sun L, Hochschild A, Darst SA, Mol Cell. 2004 Jan 16;13(1):45-53. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=14731393 14731393]
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__TOC__
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[[Category: Enterobacteria phage lambda]]
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</StructureSection>
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[[Category: Protein complex]]
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[[Category: Escherichia virus Lambda]]
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[[Category: Large Structures]]
[[Category: Thermus aquaticus]]
[[Category: Thermus aquaticus]]
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[[Category: Darst, S.A.]]
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[[Category: Darst SA]]
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[[Category: Hochschild, A.]]
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[[Category: Hochschild A]]
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[[Category: Jain, D.]]
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[[Category: Jain D]]
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[[Category: Nickels, B.E.]]
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[[Category: Nickels BE]]
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[[Category: Sun, L.]]
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[[Category: Sun L]]
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[[Category: CA]]
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[[Category: MPD]]
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[[Category: helix-turn-helix]]
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[[Category: transcription activation]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 01:37:40 2007''
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Current revision

Structure of bacteriophage lambda cI-NTD in complex with sigma-region4 of Thermus aquaticus bound to DNA

PDB ID 1rio

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