3e2e: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
 ==Crystal Structure of an Intermediate Complex of T7 RNAP and 7nt of RNA==
-<StructureSection load='3e2e' size='340' side='right' caption='[[3e2e]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
+<StructureSection load='3e2e' size='340' side='right'caption='[[3e2e]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3e2e]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacteriophage_t7 Bacteriophage t7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E2E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3E2E FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3e2e]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_phage_T7 Escherichia phage T7] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E2E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3E2E FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3e3j|3e3j]]</td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id= Bacteriophage T7])</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=3e2e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e2e OCA], [https://pdbe.org/3e2e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3e2e RCSB], [https://www.ebi.ac.uk/pdbsum/3e2e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3e2e ProSAT]</span></td></tr>
-<tr id='activity'><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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3e2e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e2e OCA], [http://pdbe.org/3e2e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3e2e RCSB], [http://www.ebi.ac.uk/pdbsum/3e2e PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/RPOL_BPT7 RPOL_BPT7]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Responsible for the transcription of the late genes of T7. It is rifampicin-resistant. It recognizes a specific promoter sequence, unwinds the double-stranded RNA to expose the coding strand for templating, initiates transcription preferentially with a purine.
+[https://www.uniprot.org/uniprot/RPOL_BPT7 RPOL_BPT7] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Responsible for the transcription of the late genes of T7. It is rifampicin-resistant. It recognizes a specific promoter sequence, unwinds the double-stranded RNA to expose the coding strand for templating, initiates transcription preferentially with a purine.
 == 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/e2/3e2e_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/e2/3e2e_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 20: / Line 19: @@
 </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=3e2e ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Structural studies of the T7 bacteriophage DNA-dependent RNA polymerase (T7 RNAP) have shown that the conformation of the amino-terminal domain changes substantially between the initiation and elongation phases of transcription, but how this transition is achieved remains unclear. We report crystal structures of T7 RNAP bound to promoter DNA containing either a 7- or an 8-nucleotide (nt) RNA transcript that illuminate intermediate states along the transition pathway. The amino-terminal domain comprises the C-helix subdomain and the promoter binding domain (PBD), which consists of two segments separated by subdomain H. The structures of the intermediate complex reveal that the PBD and the bound promoter rotate by approximately 45 degrees upon synthesis of an 8-nt RNA transcript. This allows the promoter contacts to be maintained while the active site is expanded to accommodate a growing heteroduplex. The C-helix subdomain moves modestly toward its elongation conformation, whereas subdomain H remains in its initiation- rather than its elongation-phase location, more than 70 angstroms away.
-The structure of a transcribing t7 RNA polymerase in transition from initiation to elongation.,Durniak KJ, Bailey S, Steitz TA Science. 2008 Oct 24;322(5901):553-7. PMID:18948533<ref>PMID:18948533</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3e2e" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Molecular Playground/T7 RNA Polymerase (7 mer int)|Molecular Playground/T7 RNA Polymerase (7 mer int)]]
+*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
-*[[RNA polymerase|RNA polymerase]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Bacteriophage t7]]
+[[Category: Escherichia phage T7]]
-[[Category: DNA-directed RNA polymerase]]
+[[Category: Large Structures]]
-[[Category: Bailey, S]]
+[[Category: Synthetic construct]]
-[[Category: Durniak, K J]]
+[[Category: Bailey S]]
-[[Category: Steitz, T A]]
+[[Category: Durniak KJ]]
-[[Category: Dna-directed rna polymerase]]
+[[Category: Steitz TA]]
-[[Category: Nucleotidyltransferase]]
-[[Category: T7 rna polymerase]]
-[[Category: Transcription]]
-[[Category: Transferase]]
-[[Category: Transferase-rna-dna complex]]