View source for 4w2f


==Crystal structure of the Thermus thermophilus 70S ribosome in complex with amicoumacin, mRNA and three deacylated tRNAs in the A, P and E sites==
<StructureSection load='4w2f' size='340' side='right'caption='[[4w2f]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[4w2f]] is a 20 chain structure with sequence from [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=4rb5 4rb5], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4rb6 4rb6], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4rb7 4rb7] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4rb8 4rb8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4W2F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4W2F FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</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=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=UAM:AMICOUMACIN+A'>UAM</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=4w2f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4w2f OCA], [https://pdbe.org/4w2f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4w2f RCSB], [https://www.ebi.ac.uk/pdbsum/4w2f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4w2f ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/RS2_THET8 RS2_THET8] Spans the head-body hinge region of the 30S subunit. Is loosely associated with the 30S subunit.[HAMAP-Rule:MF_00291_B]
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
We demonstrate that the antibiotic amicoumacin A (AMI) is a potent inhibitor of protein synthesis. Resistance mutations in helix 24 of the 16S rRNA mapped the AMI binding site to the small ribosomal subunit. The crystal structure of bacterial ribosome in complex with AMI solved at 2.4 A resolution revealed that the antibiotic makes contacts with universally conserved nucleotides of 16S rRNA in the E site and the mRNA backbone. Simultaneous interactions of AMI with 16S rRNA and mRNA and the in vivo experimental evidence suggest that it may inhibit the progression of the ribosome along mRNA. Consistent with this proposal, binding of AMI interferes with translocation in vitro. The inhibitory action of AMI can be partly compensated by mutations in the translation elongation factor G.

Amicoumacin a inhibits translation by stabilizing mRNA interaction with the ribosome.,Polikanov YS, Osterman IA, Szal T, Tashlitsky VN, Serebryakova MV, Kusochek P, Bulkley D, Malanicheva IA, Efimenko TA, Efremenkova OV, Konevega AL, Shaw KJ, Bogdanov AA, Rodnina MV, Dontsova OA, Mankin AS, Steitz TA, Sergiev PV Mol Cell. 2014 Nov 20;56(4):531-40. doi: 10.1016/j.molcel.2014.09.020. Epub 2014 , Oct 9. PMID:25306919<ref>PMID:25306919</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 4w2f" style="background-color:#fffaf0;"></div>

==See Also==
*[[Ribosomal protein THX 3D structures|Ribosomal protein THX 3D structures]]
*[[Ribosome 3D structures|Ribosome 3D structures]]
*[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Thermus thermophilus HB8]]
[[Category: Bogdanov AA]]
[[Category: Bulkley D]]
[[Category: Dontsova OA]]
[[Category: Efimenko TA]]
[[Category: Efremenkova OV]]
[[Category: Konevega AL]]
[[Category: Kusochek P]]
[[Category: Malanicheva IA]]
[[Category: Mankin AS]]
[[Category: Osterman IA]]
[[Category: Polikanov YS]]
[[Category: Rodnina MV]]
[[Category: Serebryakova MV]]
[[Category: Sergiev PV]]
[[Category: Shaw KJ]]
[[Category: Steitz TA]]
[[Category: Szal T]]
[[Category: Tashlitsky VN]]