View source for 5iwa


==Crystal structure of the 30S ribosomal subunit from Thermus thermophilus in complex with the GE81112 peptide antibiotic==
<StructureSection load='5iwa' size='340' side='right'caption='[[5iwa]], [[Resolution|resolution]] 3.50&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5iwa]] is a 10 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=5IWA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5IWA 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]] 3.5&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6EK:(2S,3S)-2-{[(2S)-3-(2-amino-1H-imidazol-5-yl)-2-{[(2S,4S)-5-(carbamoyloxy)-4-hydroxy-2-({[(2S,3S)-3-hydroxypiperidin-2-yl]carbonyl}amino)pentanoyl]amino}propanoyl]amino}-3-(2-chloro-1H-imidazol-5-yl)-3-hydroxypropanoic+acid'>6EK</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=5iwa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5iwa OCA], [https://pdbe.org/5iwa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5iwa RCSB], [https://www.ebi.ac.uk/pdbsum/5iwa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5iwa ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/RS7_THET8 RS7_THET8] One of the primary rRNA binding proteins, it binds directly to 3'-end of the 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center. Binds mRNA and the E site tRNA blocking its exit path in the ribosome. This blockage implies that this section of the ribosome must be able to move to release the deacetylated tRNA.[HAMAP-Rule:MF_00480_B]
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
In prokaryotic systems, the initiation phase of protein synthesis is governed by the presence of initiation factors that guide the transition of the small ribosomal subunit (30S) from an unlocked preinitiation complex (30S preIC) to a locked initiation complex (30SIC) upon the formation of a correct codon-anticodon interaction in the peptidyl (P) site. Biochemical and structural characterization of GE81112, a translational inhibitor specific for the initiation phase, indicates that the main mechanism of action of this antibiotic is to prevent P-site decoding by stabilizing the anticodon stem loop of the initiator tRNA in a distorted conformation. This distortion stalls initiation in the unlocked 30S preIC state characterized by tighter IF3 binding and a reduced association rate for the 50S subunit. At the structural level we observe that in the presence of GE81112 the h44/h45/h24a interface, which is part of the IF3 binding site and forms ribosomal intersubunit bridges, preferentially adopts a disengaged conformation. Accordingly, the findings reveal that the dynamic equilibrium between the disengaged and engaged conformations of the h44/h45/h24a interface regulates the progression of protein synthesis, acting as a molecular switch that senses and couples the 30S P-site decoding step of translation initiation to the transition from an unlocked preIC to a locked 30SIC state.

Inhibition of translation initiation complex formation by GE81112 unravels a 16S rRNA structural switch involved in P-site decoding.,Fabbretti A, Schedlbauer A, Brandi L, Kaminishi T, Giuliodori AM, Garofalo R, Ochoa-Lizarralde B, Takemoto C, Yokoyama S, Connell SR, Gualerzi CO, Fucini P Proc Natl Acad Sci U S A. 2016 Apr 19;113(16):E2286-95. doi:, 10.1073/pnas.1521156113. Epub 2016 Apr 6. PMID:27071098<ref>PMID:27071098</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5iwa" style="background-color:#fffaf0;"></div>

==See Also==
*[[Ribosomal protein THX 3D structures|Ribosomal protein THX 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Thermus thermophilus HB8]]
[[Category: Chieko N]]
[[Category: Connell SR]]
[[Category: Fucini P]]
[[Category: Kaminishi T]]
[[Category: Masahito K]]
[[Category: Ochoa-Lizarralde B]]
[[Category: Schedlbauer A]]
[[Category: Takemoto C]]
[[Category: Yokoyama S]]