6by1: Difference between revisions

Latest revision as of 12:29, 6 November 2024

E. coli pH03H9 complex

Structural highlights

6by1 is a 20 chain structure with sequence from Escherichia coli K-12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.94Å
Ligands:	MG, ZN
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RS9_ECOLI The C-terminal tail plays a role in the affinity of the 30S P site for different tRNAs. Mutations that decrease this affinity are suppressed in the 70S ribosome.^[1]

Publication Abstract from PubMed

Protein synthesis in all organisms proceeds by stepwise translocation of the ribosome along messenger RNAs (mRNAs), during which the helicase activity of the ribosome unwinds encountered structures in the mRNA. This activity is known to occur near the mRNA tunnel entrance, which is lined by ribosomal proteins uS3, uS4, and uS5. However, the mechanism(s) of mRNA unwinding by the ribosome and the possible role of these proteins in the helicase activity are not well understood. Here, we present a crystal structure of the Escherichia coli ribosome in which single-stranded mRNA is observed beyond the tunnel entrance, interacting in an extended conformation with a positively charged patch on ribosomal protein uS3 immediately outside the entrance. This apparent binding specificity for single-stranded mRNA ahead of the tunnel entrance suggests that product stabilization may play a role in the unwinding of structured mRNA by the ribosomal helicase.

Structural evidence for product stabilization by the ribosomal mRNA helicase.,Amiri H, Noller HF RNA. 2019 Mar;25(3):364-375. doi: 10.1261/rna.068965.118. Epub 2018 Dec 14. PMID:30552154^[2]

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
↑ Amiri H, Noller HF. Structural evidence for product stabilization by the ribosomal mRNA helicase. RNA. 2019 Mar;25(3):364-375. doi: 10.1261/rna.068965.118. Epub 2018 Dec 14. PMID:30552154 doi:https://dx.doi.org/10.1261/rna.068965.118

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OCA

[1] 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

[2] Amiri H, Noller HF. Structural evidence for product stabilization by the ribosomal mRNA helicase. RNA. 2019 Mar;25(3):364-375. doi: 10.1261/rna.068965.118. Epub 2018 Dec 14. PMID:30552154 doi:https://dx.doi.org/10.1261/rna.068965.118

[1]

[2]

@@ Line 3: / Line 3: @@
 <StructureSection load='6by1' size='340' side='right'caption='[[6by1]], [[Resolution|resolution]] 3.94&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6by1]] is a 22 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BY1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6BY1 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6by1]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BY1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6BY1 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]] 3.94&#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=ZN:ZINC+ION'>ZN</scene></td></tr>
@@ Line 9: / Line 9: @@
 </table>
 == Function ==
-[https://www.uniprot.org/uniprot/RL2_ECOLI RL2_ECOLI] One of the primary rRNA binding proteins. Located near the base of the L1 stalk, it is probably also mobile. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is highly controversial.[HAMAP-Rule:MF_01320_B]  In the E.coli 70S ribosome in the initiation state it has been modeled to make several contacts with the 16S rRNA (forming bridge B7b, PubMed:12809609); these contacts are broken in the model with bound EF-G.[HAMAP-Rule:MF_01320_B]
+[https://www.uniprot.org/uniprot/RS9_ECOLI RS9_ECOLI] The C-terminal tail plays a role in the affinity of the 30S P site for different tRNAs. Mutations that decrease this affinity are suppressed in the 70S ribosome.<ref>PMID:15308780</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==

6by1: Difference between revisions

Latest revision as of 12:29, 6 November 2024

E. coli pH03H9 complex

Structural highlights

Function

Publication Abstract from PubMed

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References

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