6alg: Difference between revisions

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 ==CryoEM structure of HK022 Nun - E.coli RNA polymerase elongation complex==
-<StructureSection load='6alg' size='340' side='right'caption='[[6alg]], [[Resolution|resolution]] 3.70&Aring;' scene=''>
+<SX load='6alg' size='340' side='right' viewer='molstar' caption='[[6alg]], [[Resolution|resolution]] 3.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6alg]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/Bphk0 Bphk0] and [http://en.wikipedia.org/wiki/Ecoli Ecoli]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=5up6 5up6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ALG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ALG FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6alg]] is a 9 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12], [https://en.wikipedia.org/wiki/Escherichia_phage_T7 Escherichia phage T7] and [https://en.wikipedia.org/wiki/Escherichia_virus_HK022 Escherichia virus HK022]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=5up6 5up6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ALG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ALG FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.7&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rpoA, pez, phs, sez, b3295, JW3257 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), 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=83333 ECOLI]), rpoC, tabB, b3988, JW3951 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), rpoZ, b3649, JW3624 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), nun ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10742 BPHK0])</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>
-<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'>[https://proteopedia.org/fgij/fg.htm?mol=6alg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6alg OCA], [https://pdbe.org/6alg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6alg RCSB], [https://www.ebi.ac.uk/pdbsum/6alg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6alg ProSAT]</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=6alg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6alg OCA], [http://pdbe.org/6alg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6alg RCSB], [http://www.ebi.ac.uk/pdbsum/6alg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6alg ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/RPOC_ECOLI RPOC_ECOLI]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01322] [[http://www.uniprot.org/uniprot/RPOZ_ECOLI RPOZ_ECOLI]] Promotes RNA polymerase assembly. Latches the N- and C-terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits.[HAMAP-Rule:MF_00366] [[http://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] [[http://www.uniprot.org/uniprot/RPOB_ECOLI RPOB_ECOLI]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01321]
+[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]
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Coliphage HK022 Nun blocks superinfection by coliphage lambda by stalling RNA polymerase (RNAP) translocation specifically on lambdaDeltaNA.To provide a structural framework to understand how Nun blocks RNAP translocation, we determined structures of Escherichia coli RNAP ternary elongation complexes (TECs) with and without Nun by single-particle cryo-electron microscopy. Nun fits tightly into the TEC by taking advantage of gaps between the RNAP and the nucleic acids. The C-terminal segment of Nun interacts with the RNAP beta and beta' subunits inside the RNAP active site cleft as well as with nearly every element of the nucleic-acid scaffold, essentially crosslinking the RNAP and the nucleic acids to prevent translocation, a mechanism supported by the effects of Nun amino acid substitutions. The nature of Nun interactions inside the RNAP active site cleft suggests that RNAP clamp opening is required for Nun to establish its interactions, explaining why Nun acts on paused TECs.
-Structural basis of transcription arrest by coliphage HK022 nun in an Escherichia coli RNA polymerase elongation complex.,Kang JY, Olinares PD, Chen J, Campbell EA, Mustaev A, Chait BT, Gottesman ME, Darst SA Elife. 2017 Mar 20;6. pii: e25478. doi: 10.7554/eLife.25478. PMID:28318486<ref>PMID:28318486</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 6alg" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[RNA polymerase|RNA polymerase]]
+*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
-== References ==
-<references/>
 __TOC__
-</StructureSection>
+</SX>
-[[Category: Bphk0]]
+[[Category: Escherichia coli K-12]]
-[[Category: DNA-directed RNA polymerase]]
+[[Category: Escherichia phage T7]]
-[[Category: Ecoli]]
+[[Category: Escherichia virus HK022]]
 [[Category: Large Structures]]
-[[Category: Darst, S A]]
+[[Category: Darst SA]]
-[[Category: Kang, J Y]]
+[[Category: Kang JY]]
-[[Category: Dna-dependent rna polymerase]]
-[[Category: Transcription]]
-[[Category: Transcription-dna-rna complex]]