7md7 - Revision history

OCA at 11:01, 15 November 2023

OCA — Wed, 15 Nov 2023 11:01:16 GMT

←Older revision		Revision as of 11:01, 15 November 2023
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	==See Also==		==See Also==
-	*[[Ribosomal protein THX 3D structures\|Ribosomal protein THX 3D structures]]
	*[[Ribosome 3D structures\|Ribosome 3D structures]]		*[[Ribosome 3D structures\|Ribosome 3D structures]]
	== References ==		== References ==

OCA at 16:09, 18 October 2023

OCA — Wed, 18 Oct 2023 16:09:34 GMT

←Older revision		Revision as of 16:09, 18 October 2023
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-	====	+	==Crystal structure of the Thermus thermophilus 70S ribosome in complex with triphenylphosphonium analog of chloramphenicol CAM-C4-TPP and protein Y (YfiA) at 2.80A resolution==
-	<StructureSection load='7md7' size='340' side='right'caption='[[7md7]]' scene=''>	+	<StructureSection load='7md7' size='340' side='right'caption='[[7md7]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7md7]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7MD7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7MD7 FirstGlance]. <br>
-	</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=7md7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7md7 OCA], [https://pdbe.org/7md7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7md7 RCSB], [https://www.ebi.ac.uk/pdbsum/7md7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7md7 ProSAT]</span></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]] 2.8Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0TD:(3S)-3-(METHYLSULFANYL)-L-ASPARTIC+ACID'>0TD</scene>, <scene name='pdbligand=2MA:2-METHYLADENOSINE-5-MONOPHOSPHATE'>2MA</scene>, <scene name='pdbligand=2MG:2N-METHYLGUANOSINE-5-MONOPHOSPHATE'>2MG</scene>, <scene name='pdbligand=2MU:2,5-DIMETHYLURIDINE-5-MONOPHOSPHATE'>2MU</scene>, <scene name='pdbligand=4OC:4N,O2-METHYLCYTIDINE-5-MONOPHOSPHATE'>4OC</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=7MG:7N-METHYL-8-HYDROGUANOSINE-5-MONOPHOSPHATE'>7MG</scene>, <scene name='pdbligand=ARG:ARGININE'>ARG</scene>, <scene name='pdbligand=M2G:N2-DIMETHYLGUANOSINE-5-MONOPHOSPHATE'>M2G</scene>, <scene name='pdbligand=MA6:6N-DIMETHYLADENOSINE-5-MONOPHOSHATE'>MA6</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=UR3:3-METHYLURIDINE-5-MONOPHOSHATE'>UR3</scene>, <scene name='pdbligand=YXM:N-[(1R,2R)-1,3-dihydroxy-1-(4-nitrophenyl)propan-2-yl]-5-(triphenyl-lambda~5~-phosphanyl)pentanamide'>YXM</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=7md7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7md7 OCA], [https://pdbe.org/7md7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7md7 RCSB], [https://www.ebi.ac.uk/pdbsum/7md7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7md7 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/RL2_THET8 RL2_THET8] One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial (By similarity). Makes several contacts with the 16S rRNA (forming bridge B7b) in the 70S ribosome.[HAMAP-Rule:MF_01320_B]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Chloramphenicol (CHL) is a ribosome-targeting antibiotic that binds to the peptidyl transferase center (PTC) of the bacterial ribosome and inhibits peptide bond formation. As an approach for modifying and potentially improving the properties of this inhibitor, we explored ribosome binding and inhibitory properties of a semi-synthetic triphenylphosphonium analog of CHL-CAM-C4-TPP. Our data demonstrate that this compound exhibits a ~5-fold stronger affinity for the bacterial ribosome and higher potency as an in vitro protein synthesis inhibitor compared to CHL. The X-ray crystal structure of the Thermus thermophilus 70S ribosome in complex with CAM-C4-TPP reveals that, while its amphenicol moiety binds at the PTC in a fashion identical to CHL, the C4-TPP tail adopts an extended propeller-like conformation within the ribosome exit tunnel where it establishes multiple hydrophobic Van der Waals interactions with the rRNA. The synthesized compound represents a promising chemical scaffold for further development by medicinal chemists because it simultaneously targets the two key functional centers of the bacterial ribosome-PTC and peptide exit tunnel.
		+
		+	Binding and Action of Triphenylphosphonium Analog of Chloramphenicol upon the Bacterial Ribosome.,Chen CW, Pavlova JA, Lukianov DA, Tereshchenkov AG, Makarov GI, Khairullina ZZ, Tashlitsky VN, Paleskava A, Konevega AL, Bogdanov AA, Osterman IA, Sumbatyan NV, Polikanov YS Antibiotics (Basel). 2021 Apr 5;10(4):390. doi: 10.3390/antibiotics10040390. PMID:33916420<ref>PMID:33916420</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7md7" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ribosomal protein THX 3D structures\|Ribosomal protein THX 3D structures]]
		+	*[[Ribosome 3D structures\|Ribosome 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Z-~~disk~~]]	+	[[Category: Thermus thermophilus HB8]]
		+	[[Category: Bogdanov AA]]
		+	[[Category: Chen C-W]]
		+	[[Category: Khairullina ZZ]]
		+	[[Category: Konevega AL]]
		+	[[Category: Lukianov DA]]
		+	[[Category: Makarov GI]]
		+	[[Category: Osterman IA]]
		+	[[Category: Paleskava A]]
		+	[[Category: Pavlova JA]]
		+	[[Category: Polikanov YS]]
		+	[[Category: Sumbatyan NV]]
		+	[[Category: Tashlitsky VN]]
		+	[[Category: Tereshchenkov AG]]

OCA at 08:24, 21 April 2021

OCA — Wed, 21 Apr 2021 08:24:57 GMT

←Older revision		Revision as of 08:24, 21 April 2021
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7md7 ~~is ON HOLD~~	+	====
-		+	<StructureSection load='7md7' size='340' side='right'caption='[[7md7]]' scene=''>
-	~~Authors~~: ~~Chen, C~~.-W.~~, Pavlova, J~~.A.~~, Lukianov, D~~.A.~~, Tereshchenkov, A.G., Makarov, G.I., Khairullina, Z.Z., Tashlitsky, V.N., Paleskava, A., Konevega, A.L., Bogdanov, A.A., Osterman, I.A., Sumbatyan, N.V., Polikanov, Y.S~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure of the Thermus thermophilus 70S ribosome in complex with triphenylphosphonium analog of chloramphenicol CAM-C4-TPP and protein Y (YfiA) at 2.80A resolution~~	+	</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=7md7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7md7 OCA], [https://pdbe.org/7md7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7md7 RCSB], [https://www.ebi.ac.uk/pdbsum/7md7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7md7 ProSAT]</span></td></tr>
-	[~~[Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[~~[Category~~: ~~Osterman, I~~.A]]	+	__TOC__
-	~~[[Category: Konevega~~, ~~A.L]]~~	+	</StructureSection>
-	[~~[Category~~: ~~Sumbatyan, N~~.V]]	+	[[Category: Large Structures]]
-	~~[[Category: Bogdanov~~, ~~A.A]]~~	+	[[Category: Z-disk]]
-	[~~[Category~~: ~~Tashlitsky, V~~.N]]	+
-	~~[[Category: Tereshchenkov~~, ~~A.G]]~~	+
-	[~~[Category~~: ~~Makarov, G~~.I]]	+
-	~~[[Category: Polikanov~~, ~~Y.S]]~~	+
-	[~~[Category~~: ~~Chen, C~~.-W]]	+
-	~~[[Category: Paleskava, A]]~~	+
-	~~[[Category: Khairullina, Z.Z]]~~	+
-	[[Category: ~~Lukianov, D.A~~]]	+
-	[[Category: ~~Pavlova, J.A~~]]	+

OCA: Protected "7md7" [edit=sysop:move=sysop]

OCA — Wed, 14 Apr 2021 05:41:13 GMT

Protected "7md7" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:41, 14 April 2021

OCA: New page: '''Unreleased structure''' The entry 7md7 is ON HOLD Authors: Chen, C.-W., Pavlova, J.A., Lukianov, D.A., Tereshchenkov, A.G., Makarov, G.I., Khairullina, Z.Z., Tashlitsky, V.N., Palesk...

OCA — Wed, 14 Apr 2021 05:41:12 GMT

New page: '''Unreleased structure''' The entry 7md7 is ON HOLD Authors: Chen, C.-W., Pavlova, J.A., Lukianov, D.A., Tereshchenkov, A.G., Makarov, G.I., Khairullina, Z.Z., Tashlitsky, V.N., Palesk...

New page

'''Unreleased structure'''

The entry 7md7 is ON HOLD

Authors: Chen, C.-W., Pavlova, J.A., Lukianov, D.A., Tereshchenkov, A.G., Makarov, G.I., Khairullina, Z.Z., Tashlitsky, V.N., Paleskava, A., Konevega, A.L., Bogdanov, A.A., Osterman, I.A., Sumbatyan, N.V., Polikanov, Y.S.

Description: Crystal structure of the Thermus thermophilus 70S ribosome in complex with triphenylphosphonium analog of chloramphenicol CAM-C4-TPP and protein Y (YfiA) at 2.80A resolution
[[Category: Unreleased Structures]]
[[Category: Osterman, I.A]]
[[Category: Konevega, A.L]]
[[Category: Sumbatyan, N.V]]
[[Category: Bogdanov, A.A]]
[[Category: Tashlitsky, V.N]]
[[Category: Tereshchenkov, A.G]]
[[Category: Makarov, G.I]]
[[Category: Polikanov, Y.S]]
[[Category: Chen, C.-W]]
[[Category: Paleskava, A]]
[[Category: Khairullina, Z.Z]]
[[Category: Lukianov, D.A]]
[[Category: Pavlova, J.A]]