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4v52

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Crystal structure of the bacterial ribosome from Escherichia coli in complex with neomycin.

Structural highlights

4v52 is a 20 chain structure with sequence from Escherichia coli. This structure supersedes the now removed PDB entries 2qal, 2qam, 2qan and 2qao. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.21Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RS13_ECOLI Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA.^[1] In the E.coli 70S ribosome in the initiation state (PubMed:12809609) was modeled to contact the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; bridge B1a is broken in the model with bound EF-G, while the protein-protein contacts between S13 and L5 in B1b change (PubMed:12809609). The 23S rRNA contact site in bridge B1a is modeled to differ in different ribosomal states (PubMed:16272117), contacting alternately S13 or S19. In the two 3.5 angstroms resolved ribosome structures (PubMed:12859903) the contacts between L5, S13 and S19 bridge B1b are different, confirming the dynamic nature of this interaction. Bridge B1a is not visible in the crystallized ribosomes due to 23S rRNA disorder.^[2] Contacts the tRNAs in the A and P sites.^[3] The C-terminal tail plays a role in the affinity of the 30S P site for different tRNAs.^[4]

Publication Abstract from PubMed

Aminoglycosides are widely used antibiotics that cause messenger RNA decoding errors, block mRNA and transfer RNA translocation, and inhibit ribosome recycling. Ribosome recycling follows the termination of protein synthesis and is aided by ribosome recycling factor (RRF) in bacteria. The molecular mechanism by which aminoglycosides inhibit ribosome recycling is unknown. Here we show in X-ray crystal structures of the Escherichia coli 70S ribosome that RRF binding causes RNA helix H69 of the large ribosomal subunit, which is crucial for subunit association, to swing away from the subunit interface. Aminoglycosides bind to H69 and completely restore the contacts between ribosomal subunits that are disrupted by RRF. These results provide a structural explanation for aminoglycoside inhibition of ribosome recycling.

Structural basis for aminoglycoside inhibition of bacterial ribosome recycling.,Borovinskaya MA, Pai RD, Zhang W, Schuwirth BS, Holton JM, Hirokawa G, Kaji H, Kaji A, Cate JH Nat Struct Mol Biol. 2007 Aug;14(8):727-32. Epub 2007 Jul 29. PMID:17660832^[5]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Hoang L, Fredrick K, Noller HF. Creating ribosomes with an all-RNA 30S subunit P site. Proc Natl Acad Sci U S A. 2004 Aug 24;101(34):12439-43. Epub 2004 Aug 12. PMID:15308780 doi:10.1073/pnas.0405227101
↑ Hoang L, Fredrick K, Noller HF. Creating ribosomes with an all-RNA 30S subunit P site. Proc Natl Acad Sci U S A. 2004 Aug 24;101(34):12439-43. Epub 2004 Aug 12. PMID:15308780 doi:10.1073/pnas.0405227101
↑ Hoang L, Fredrick K, Noller HF. Creating ribosomes with an all-RNA 30S subunit P site. Proc Natl Acad Sci U S A. 2004 Aug 24;101(34):12439-43. Epub 2004 Aug 12. PMID:15308780 doi:10.1073/pnas.0405227101
↑ Hoang L, Fredrick K, Noller HF. Creating ribosomes with an all-RNA 30S subunit P site. Proc Natl Acad Sci U S A. 2004 Aug 24;101(34):12439-43. Epub 2004 Aug 12. PMID:15308780 doi:10.1073/pnas.0405227101
↑ Borovinskaya MA, Pai RD, Zhang W, Schuwirth BS, Holton JM, Hirokawa G, Kaji H, Kaji A, Cate JH. Structural basis for aminoglycoside inhibition of bacterial ribosome recycling. Nat Struct Mol Biol. 2007 Aug;14(8):727-32. Epub 2007 Jul 29. PMID:17660832 doi:http://dx.doi.org/10.1038/nsmb1271

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4v52"

@@ Line 4: / Line 4: @@
 == Structural highlights ==
 <table><tr><td colspan='2'>[[4v52]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2qal 2qal], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2qam 2qam], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2qan 2qan] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2qao 2qao]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4V52 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4V52 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NMY:NEOMYCIN'>NMY</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]] 3.21&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NMY:NEOMYCIN'>NMY</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=4v52 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4v52 OCA], [https://pdbe.org/4v52 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4v52 RCSB], [https://www.ebi.ac.uk/pdbsum/4v52 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4v52 ProSAT]</span></td></tr>
 </table>

4v52

From Proteopedia

Current revision

Crystal structure of the bacterial ribosome from Escherichia coli in complex with neomycin.

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

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