3lpe: Difference between revisions

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-[[Image:3lpe.png|left|200px]]
-{{STRUCTURE_3lpe|  PDB=3lpe  |  SCENE=  }}
+==Crystal structure of Spt4/5NGN heterodimer complex from Methanococcus jannaschii==
+<StructureSection load='3lpe' size='340' side='right'caption='[[3lpe]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3lpe]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LPE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LPE FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=3lpe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lpe OCA], [https://pdbe.org/3lpe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3lpe RCSB], [https://www.ebi.ac.uk/pdbsum/3lpe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3lpe ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SPT5_METJA SPT5_METJA] Stimulates transcription elongation.[HAMAP-Rule:MF_00950]<ref>PMID:20197319</ref>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lp/3lpe_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </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/main_output.php?pdb_ID=3lpe ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Spt5 is the only known RNA polymerase-associated factor that is conserved in all three domains of life. We have solved the structure of the Methanococcus jannaschii Spt4/5 complex by X-ray crystallography, and characterized its function and interaction with the archaeal RNAP in a wholly recombinant in vitro transcription system. Archaeal Spt4 and Spt5 form a stable complex that associates with RNAP independently of the DNA-RNA scaffold of the elongation complex. The association of Spt4/5 with RNAP results in a stimulation of transcription processivity, both in the absence and the presence of the non-template strand. A domain deletion analysis reveals the molecular anatomy of Spt4/5--the Spt5 Nus-G N-terminal (NGN) domain is the effector domain of the complex that both mediates the interaction with RNAP and is essential for its elongation activity. Using a mutagenesis approach, we have identified a hydrophobic pocket on the Spt5 NGN domain as binding site for RNAP, and reciprocally the RNAP clamp coiled-coil motif as binding site for Spt4/5.
-===Crystal structure of Spt4/5NGN heterodimer complex from Methanococcus jannaschii===
+Spt4/5 stimulates transcription elongation through the RNA polymerase clamp coiled-coil motif.,Hirtreiter A, Damsma GE, Cheung AC, Klose D, Grohmann D, Vojnic E, Martin AC, Cramer P, Werner F Nucleic Acids Res. 2010 Jul 1;38(12):4040-51. Epub 2010 Mar 2. PMID:20197319<ref>PMID:20197319</ref>
-{{ABSTRACT_PUBMED_20197319}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 3lpe" style="background-color:#fffaf0;"></div>
-[[3lpe]] is a 8 chain structure of [[RNA polymerase]] with sequence from [http://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LPE OCA].
 ==See Also==
-*[[RNA polymerase|RNA polymerase]]
+*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:020197319</ref><references group="xtra"/>
+__TOC__
-[[Category: DNA-directed RNA polymerase]]
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Methanocaldococcus jannaschii]]
-[[Category: Cheung, A C.M.]]
+[[Category: Cheung ACM]]
-[[Category: Cramer, P.]]
+[[Category: Cramer P]]
-[[Category: Damsma, G E.]]
+[[Category: Damsma GE]]
-[[Category: Grohmann, D.]]
+[[Category: Grohmann D]]
-[[Category: Hirtreiter, A.]]
+[[Category: Hirtreiter A]]
-[[Category: Klose, D.]]
+[[Category: Klose D]]
-[[Category: Martin, A C.R.]]
+[[Category: Martin ACR]]
-[[Category: Vojnic, E.]]
+[[Category: Vojnic E]]
-[[Category: Werner, F.]]
+[[Category: Werner F]]
-[[Category: Archaea]]
-[[Category: Dna-directed rna polymerase]]
-[[Category: Evolution]]
-[[Category: Metal-binding]]
-[[Category: Nucleotidyltransferase]]
-[[Category: Nusg]]
-[[Category: Spt4]]
-[[Category: Spt5]]
-[[Category: Transcription]]
-[[Category: Transcription regulation]]
-[[Category: Transferase]]
-[[Category: Zinc-finger]]