4dr6: Difference between revisions

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-[[Image:4dr6.jpg|left|200px]]
-{{STRUCTURE_4dr6|  PDB=4dr6  |  SCENE=  }}
+==Crystal structure of the Thermus thermophilus (HB8) 30S ribosomal subunit with codon, near-cognate transfer RNA anticodon stem-loop mismatched at the first codon position and streptomycin bound==
+<StructureSection load='4dr6' size='340' side='right'caption='[[4dr6]], [[Resolution|resolution]] 3.30&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[4dr6]] 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=4DR6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DR6 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]] 3.3&#8491;</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=2MG:2N-METHYLGUANOSINE-5-MONOPHOSPHATE'>2MG</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=7MG:7N-METHYL-8-HYDROGUANOSINE-5-MONOPHOSPHATE'>7MG</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=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=SRY:STREPTOMYCIN'>SRY</scene>, <scene name='pdbligand=UR3:3-METHYLURIDINE-5-MONOPHOSHATE'>UR3</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=4dr6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dr6 OCA], [https://pdbe.org/4dr6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4dr6 RCSB], [https://www.ebi.ac.uk/pdbsum/4dr6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4dr6 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 ==
+During protein synthesis, the ribosome selects aminoacyl-transfer RNAs with anticodons matching the messenger RNA codon present in the A site of the small ribosomal subunit. The aminoglycoside antibiotic streptomycin disrupts decoding by binding close to the site of codon recognition. Here we use X-ray crystallography to define the impact of streptomycin on the decoding site of the Thermus thermophilus 30S ribosomal subunit in complexes with cognate or near-cognate anticodon stem-loop analogues and messenger RNA. Our crystal structures display a significant local distortion of 16S ribosomal RNA induced by streptomycin, including the crucial bases A1492 and A1493 that participate directly in codon recognition. Consistent with kinetic data, we observe that streptomycin stabilizes the near-cognate anticodon stem-loop analogue complex, while destabilizing the cognate anticodon stem-loop analogue complex. These data reveal how streptomycin disrupts the recognition of cognate anticodon stem-loop analogues and yet improves recognition of a near-cognate anticodon stem-loop analogue.
-===Crystal structure of the Thermus thermophilus (HB8) 30S ribosomal subunit with codon, near-cognate transfer RNA anticodon stem-loop mismatched at the first codon position and streptomycin bound===
+A structural basis for streptomycin-induced misreading of the genetic code.,Demirci H, Murphy F 4th, Murphy E, Gregory ST, Dahlberg AE, Jogl G Nat Commun. 2013 Jan 15;4:1355. doi: 10.1038/ncomms2346. PMID:23322043<ref>PMID:23322043</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 4dr6" style="background-color:#fffaf0;"></div>
-==About this Structure==
+==See Also==
-[[4dr6]] is a 25 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DR6 OCA].
+*[[Ribosomal protein THX 3D structures|Ribosomal protein THX 3D structures]]
-[[Category: Thermus thermophilus]]
+*[[Ribosome 3D structures|Ribosome 3D structures]]
-[[Category: Dahlberg, A E.]]
+== References ==
-[[Category: Demirci, H.]]
+<references/>
-[[Category: Gregory, S T.]]
+__TOC__
-[[Category: IV, F Murphy.]]
+</StructureSection>
-[[Category: Jogl, G.]]
+[[Category: Large Structures]]
-[[Category: Murphy, E.]]
+[[Category: Thermus thermophilus HB8]]
-[[Category: Antibiotic resistance]]
+[[Category: Dahlberg AE]]
-[[Category: Decoding]]
+[[Category: Demirci H]]
-[[Category: Ribosome-antibiotic complex]]
+[[Category: Gregory ST]]
-[[Category: Rna structure]]
+[[Category: Jogl G]]
-[[Category: Streptomycin]]
+[[Category: Murphy E]]
+[[Category: Murphy IV F]]