View source for 6kf4


==Cryo-EM structure of Thermococcus kodakarensis RNA polymerase==
<StructureSection load='6kf4' size='340' side='right'caption='[[6kf4]], [[Resolution|resolution]] 3.97&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[6kf4]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_kodakarensis_KOD1 Thermococcus kodakarensis KOD1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KF4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6KF4 FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.97&#8491;</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6kf4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kf4 OCA], [https://pdbe.org/6kf4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6kf4 RCSB], [https://www.ebi.ac.uk/pdbsum/6kf4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6kf4 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/RPO12_THEKO RPO12_THEKO] DNA-dependent RNA polymerase (RNAP) catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_00615]
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Opening of the DNA binding cleft of cellular RNA polymerase (RNAP) is necessary for transcription initiation but the underlying molecular mechanism is not known. Here, we report on the cryo-electron microscopy structures of the RNAP, RNAP-TFEalpha binary, and RNAP-TFEalpha-promoter DNA ternary complexes from archaea, Thermococcus kodakarensis (Tko). The structures reveal that TFEalpha bridges the RNAP clamp and stalk domains to open the DNA binding cleft. Positioning of promoter DNA into the cleft closes it while maintaining the TFEalpha interactions with the RNAP mobile modules. The structures and photo-crosslinking results also suggest that the conserved aromatic residue in the extended winged-helix domain of TFEalpha interacts with promoter DNA to stabilize the transcription bubble. This study provides a structural basis for the functions of TFEalpha and elucidates the mechanism by which the DNA binding cleft is opened during transcription initiation in the stalk-containing RNAPs, including archaeal and eukaryotic RNAPs.

Direct binding of TFEalpha opens DNA binding cleft of RNA polymerase.,Jun SH, Hyun J, Cha JS, Kim H, Bartlett MS, Cho HS, Murakami KS Nat Commun. 2020 Nov 30;11(1):6123. doi: 10.1038/s41467-020-19998-x. PMID:33257704<ref>PMID:33257704</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6kf4" style="background-color:#fffaf0;"></div>

==See Also==
*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
*[[Transcription initiation factors 3D structures|Transcription initiation factors 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Thermococcus kodakarensis KOD1]]
[[Category: Bartlett MS]]
[[Category: Cha JS]]
[[Category: Cho H-S]]
[[Category: Hyun J]]
[[Category: Jeong H]]
[[Category: Jun S-H]]
[[Category: Kim H]]
[[Category: Murakami KS]]