10ml: Difference between revisions

Line 1:

~~'''Unreleased structure'''~~

~~The entry~~ 10ml is ~~ON HOLD until Paper~~ Publication

==AAP-SO2 bound Open Mtb-EC: Cryo-EM structure of Mtb RNAP elongation complex (substrate loading mimic) with an open active site (open TL and RH-FL)==

== Structural highlights ==

<table><tr><td colspan='2'>[[10ml]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=10ML OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=10ML 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]] 3Å</td></tr>

<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A1BNV:~{N}-[(2~{R})-1-[[2-[1,1-bis(oxidanylidene)-1,4-thiazinan-4-yl]phenyl]amino]-1-oxidanylidene-3-phenyl-propan-2-yl]-2-fluoranyl-benzamide'>A1BNV</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <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=10ml FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=10ml OCA], [https://pdbe.org/10ml PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=10ml RCSB], [https://www.ebi.ac.uk/pdbsum/10ml PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=10ml ProSAT]</span></td></tr>

</table>

== Function ==

[https://www.uniprot.org/uniprot/RPOB_MYCTU RPOB_MYCTU] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01321]

== Publication Abstract from PubMed ==

The nucleotide-addition cycle (NAC) of multi-subunit DNA-dependent RNA polymerases (RNAPs) involves coordinated conformational changes in conserved active-site structural elements, including the trigger loop (TL). The TL is open (unfolded) in most RNAP structures but can close (fold) in substrate-bound (post- or pre-translocated) states of the RNAP, promoting catalysis. TL closure has been associated with closure of another conserved structural element, the Rim-Helices/F-loop (RH-FL), but the role of the RH-FL in the NAC is unclear. Antibiotic leads CBR9379 and AAP-SO (2) inhibit the Escherichia coli and Mycobacterium tuberculosis RNAPs, respectively, by binding in a pocket formed by the bridge helix and RH-FL. The precise mechanism of action for these inhibitors is yet to be defined. We present cryo-electron microscopy structures showing that both compounds inhibit the RNAP NAC by preventing RH-FL closure, thereby allosterically destabilizing the closed TL. This work reveals a conserved mechanistic principle of RNAP catalysis across all domains of life and provides new insight for antibiotic design.

~~Authors~~:

RNA polymerase inhibitors reveal active-site motions essential for the nucleotide-addition cycle.,Dhingra Y, Landick R, Campbell EA, Darst SA bioRxiv [Preprint]. 2026 Apr 7:2026.04.06.716786. doi: , 10.64898/2026.04.06.716786. PMID:41993335<ref>PMID:41993335</ref>

~~Description~~:

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

[[Category: ~~Unreleased~~ Structures]]

</div>

== References ==

__TOC__

</StructureSection>

[[Category: Escherichia coli]]

[[Category: Large Structures]]

[[Category: Mycobacterium tuberculosis]]

[[Category: Darst SA]]

[[Category: Dhingra Y]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 10ml is ON HOLD  until Paper Publication
+==AAP-SO2 bound Open Mtb-EC: Cryo-EM structure of Mtb RNAP elongation complex (substrate loading mimic) with an open active site (open TL and RH-FL)==
+<StructureSection load='10ml' size='340' side='right'caption='[[10ml]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[10ml]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=10ML OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=10ML 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&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A1BNV:~{N}-[(2~{R})-1-[[2-[1,1-bis(oxidanylidene)-1,4-thiazinan-4-yl]phenyl]amino]-1-oxidanylidene-3-phenyl-propan-2-yl]-2-fluoranyl-benzamide'>A1BNV</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <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=10ml FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=10ml OCA], [https://pdbe.org/10ml PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=10ml RCSB], [https://www.ebi.ac.uk/pdbsum/10ml PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=10ml ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RPOB_MYCTU RPOB_MYCTU] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01321]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The nucleotide-addition cycle (NAC) of multi-subunit DNA-dependent RNA polymerases (RNAPs) involves coordinated conformational changes in conserved active-site structural elements, including the trigger loop (TL). The TL is open (unfolded) in most RNAP structures but can close (fold) in substrate-bound (post- or pre-translocated) states of the RNAP, promoting catalysis. TL closure has been associated with closure of another conserved structural element, the Rim-Helices/F-loop (RH-FL), but the role of the RH-FL in the NAC is unclear. Antibiotic leads CBR9379 and AAP-SO (2) inhibit the Escherichia coli and Mycobacterium tuberculosis RNAPs, respectively, by binding in a pocket formed by the bridge helix and RH-FL. The precise mechanism of action for these inhibitors is yet to be defined. We present cryo-electron microscopy structures showing that both compounds inhibit the RNAP NAC by preventing RH-FL closure, thereby allosterically destabilizing the closed TL. This work reveals a conserved mechanistic principle of RNAP catalysis across all domains of life and provides new insight for antibiotic design.
-Authors:
+RNA polymerase inhibitors reveal active-site motions essential for the nucleotide-addition cycle.,Dhingra Y, Landick R, Campbell EA, Darst SA bioRxiv [Preprint]. 2026 Apr 7:2026.04.06.716786. doi: , 10.64898/2026.04.06.716786. PMID:41993335<ref>PMID:41993335</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 10ml" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Escherichia coli]]
+[[Category: Large Structures]]
+[[Category: Mycobacterium tuberculosis]]
+[[Category: Darst SA]]
+[[Category: Dhingra Y]]