4dr2: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older editNewer edit →
No edit summary
No edit summary
Line 1: Line 1:
{{Large structure}}
==Crystal structure of the Thermus thermophilus (HB8) 30S ribosomal subunit with multiple copies of paromomycin molecules bound==
{{STRUCTURE_4dr2|  PDB=4dr2  |  SCENE=  }}
<StructureSection load='4dr2' size='340' side='right' caption='[[4dr2]], [[Resolution|resolution]] 3.25&Aring;' scene=''>
===Crystal structure of the Thermus thermophilus (HB8) 30S ribosomal subunit with multiple copies of paromomycin molecules bound===
== Structural highlights ==
{{ABSTRACT_PUBMED_23322043}}
<table><tr><td colspan='2'>[[4dr2]] is a 21 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=4DR2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DR2 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PAR:PAROMOMYCIN'>PAR</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><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=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=UR3:3-METHYLURIDINE-5-MONOPHOSHATE'>UR3</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4dr1|4dr1]], [[4dr3|4dr3]], [[4dr4|4dr4]], [[4dr5|4dr5]], [[4dr6|4dr6]], [[4dr7|4dr7]]</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4dr2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dr2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4dr2 RCSB], [http://www.ebi.ac.uk/pdbsum/4dr2 PDBsum]</span></td></tr>
</table>
<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.


==About this Structure==
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>
[[4dr2]] is a 21 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=4DR2 OCA].


==See Also==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
*[[Ribosomal protein S10|Ribosomal protein S10]]
</div>
*[[Ribosomal protein S11|Ribosomal protein S11]]
== References ==
*[[Ribosomal protein S6|Ribosomal protein S6]]
<references/>
*[[Ribosomal protein S7|Ribosomal protein S7]]
__TOC__
*[[Ribosomal protein S8|Ribosomal protein S8]]
</StructureSection>
*[[Ribosomal protein S9|Ribosomal protein S9]]
[[Category: Thermus thermophilus]]
[[Category: Thermus thermophilus]]
[[Category: Dahlberg, A E.]]
[[Category: Dahlberg, A E]]
[[Category: Demirci, H.]]
[[Category: Demirci, H]]
[[Category: Gregory, S T.]]
[[Category: Gregory, S T]]
[[Category: IV, F Murphy.]]
[[Category: IV, F Murphy]]
[[Category: Jogl, G.]]
[[Category: Jogl, G]]
[[Category: Murphy, E.]]
[[Category: Murphy, E]]
[[Category: Antibiotic resistance]]
[[Category: Antibiotic resistance]]
[[Category: Decoding]]
[[Category: Decoding]]

Revision as of 11:42, 18 December 2014

Crystal structure of the Thermus thermophilus (HB8) 30S ribosomal subunit with multiple copies of paromomycin molecules boundCrystal structure of the Thermus thermophilus (HB8) 30S ribosomal subunit with multiple copies of paromomycin molecules bound

Structural highlights

4dr2 is a 21 chain structure with sequence from Thermus thermophilus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:, ,
NonStd Res:, , , , , , , ,
Resources:FirstGlance, OCA, RCSB, PDBsum

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.

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[1]

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

References

  1. ↑ Demirci H, Murphy F 4th, Murphy E, Gregory ST, Dahlberg AE, Jogl G. A structural basis for streptomycin-induced misreading of the genetic code. Nat Commun. 2013 Jan 15;4:1355. doi: 10.1038/ncomms2346. PMID:23322043 doi:http://dx.doi.org/10.1038/ncomms2346

4dr2, resolution 3.25Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=4dr2&oldid=2110395"