4w2i: Difference between revisions
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== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4w2i]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4rbh 4rbh], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4rbi 4rbi], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4rbj 4rbj] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4rbk 4rbk]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4W2I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4W2I FirstGlance]. <br> | <table><tr><td colspan='2'>[[4w2i]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4rbh 4rbh], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4rbi 4rbi], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4rbj 4rbj] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4rbk 4rbk]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4W2I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4W2I FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4SU:4-THIOURIDINE-5-MONOPHOSPHATE'>4SU</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=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MIA:2-METHYLTHIO-N6-ISOPENTENYL-ADENOSINE-5-MONOPHOSPHATE'>MIA</scene>, <scene name='pdbligand=NEG:NEGAMYCIN'>NEG</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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">X-ray diffraction, [[Resolution|Resolution]] 2.7Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4SU:4-THIOURIDINE-5-MONOPHOSPHATE'>4SU</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=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MIA:2-METHYLTHIO-N6-ISOPENTENYL-ADENOSINE-5-MONOPHOSPHATE'>MIA</scene>, <scene name='pdbligand=NEG:NEGAMYCIN'>NEG</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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=4w2i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4w2i OCA], [https://pdbe.org/4w2i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4w2i RCSB], [https://www.ebi.ac.uk/pdbsum/4w2i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4w2i ProSAT]</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=4w2i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4w2i OCA], [https://pdbe.org/4w2i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4w2i RCSB], [https://www.ebi.ac.uk/pdbsum/4w2i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4w2i ProSAT]</span></td></tr> | ||
</table> | </table> | ||
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==See Also== | ==See Also== | ||
*[[Ribosomal protein THX 3D structures|Ribosomal protein THX 3D structures]] | |||
*[[Ribosome 3D structures|Ribosome 3D structures]] | |||
*[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]] | *[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]] | ||
== References == | == References == | ||
Latest revision as of 03:51, 28 December 2023
Crystal structure of the Thermus thermophilus 70S ribosome in complex with negamycin, mRNA and three deacylated tRNAs in the A, P and E sitesCrystal structure of the Thermus thermophilus 70S ribosome in complex with negamycin, mRNA and three deacylated tRNAs in the A, P and E sites
Structural highlights
FunctionRS3_THET8 Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01309_B] Publication Abstract from PubMedNegamycin (NEG) is a ribosome-targeting antibiotic that exhibits clinically promising activity. Its binding site and mode of action have remained unknown. We solved the structure of the Thermus thermophilus ribosome bound to mRNA and three tRNAs, in complex with NEG. The drug binds to both small and large ribosomal subunits at nine independent sites. Resistance mutations in the 16S rRNA unequivocally identified the binding site in the vicinity of the conserved helix 34 (h34) in the small subunit as the primary site of antibiotic action in the bacterial and, possibly, eukaryotic ribosome. At this site, NEG contacts 16S rRNA as well as the anticodon loop of the A-site tRNA. Although the NEG site of action overlaps with that of tetracycline (TET), the two antibiotics exhibit different activities: while TET sterically hinders binding of aminoacyl-tRNA to the ribosome, NEG stabilizes its binding, thereby inhibiting translocation and stimulating miscoding. Negamycin Interferes with Decoding and Translocation by Simultaneous Interaction with rRNA and tRNA.,Polikanov YS, Szal T, Jiang F, Gupta P, Matsuda R, Shiozuka M, Steitz TA, Vazquez-Laslop N, Mankin AS Mol Cell. 2014 Nov 20;56(4):541-50. doi: 10.1016/j.molcel.2014.09.021. Epub 2014 , Oct 9. PMID:25306922[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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