7a05: Difference between revisions

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==NMR structure of D3-D4 domains of Vibrio vulnificus ribosomal protein S1==
==NMR structure of D3-D4 domains of Vibrio vulnificus ribosomal protein S1==
<StructureSection load='7a05' size='340' side='right'caption='[[7a05]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
<StructureSection load='7a05' size='340' side='right'caption='[[7a05]]' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[7a05]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_27562 Atcc 27562]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7A05 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7A05 FirstGlance]. <br>
<table><tr><td colspan='2'>[[7a05]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_vulnificus Vibrio vulnificus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7A05 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7A05 FirstGlance]. <br>
</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rpsA, CRN34_17730, CRN52_15765, D8T49_21570, JS86_12670 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=672 ATCC 27562])</td></tr>
</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=7a05 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7a05 OCA], [https://pdbe.org/7a05 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7a05 RCSB], [https://www.ebi.ac.uk/pdbsum/7a05 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7a05 ProSAT]</span></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=7a05 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7a05 OCA], [https://pdbe.org/7a05 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7a05 RCSB], [https://www.ebi.ac.uk/pdbsum/7a05 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7a05 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/A0A087IKW3_VIBVL A0A087IKW3_VIBVL]] Binds mRNA; thus facilitating recognition of the initiation point. It is needed to translate mRNA with a short Shine-Dalgarno (SD) purine-rich sequence.[PIRNR:PIRNR002111]  
[https://www.uniprot.org/uniprot/A0A3Q0L6Y6_VIBVU A0A3Q0L6Y6_VIBVU] Binds mRNA; thus facilitating recognition of the initiation point. It is needed to translate mRNA with a short Shine-Dalgarno (SD) purine-rich sequence.[PIRNR:PIRNR002111]
<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
== Publication Abstract from PubMed ==
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</div>
</div>
<div class="pdbe-citations 7a05" style="background-color:#fffaf0;"></div>
<div class="pdbe-citations 7a05" style="background-color:#fffaf0;"></div>
==See Also==
*[[Ribosomal protein S1|Ribosomal protein S1]]
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Atcc 27562]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Cetiner, E C]]
[[Category: Vibrio vulnificus]]
[[Category: Fuertig, B]]
[[Category: Cetiner EC]]
[[Category: Jonker, H R.A]]
[[Category: Fuertig B]]
[[Category: Matzel, T]]
[[Category: Jonker HRA]]
[[Category: Qureshi, N S]]
[[Category: Matzel T]]
[[Category: Schnieders, S]]
[[Category: Qureshi NS]]
[[Category: Schwalbe, H]]
[[Category: Schnieders S]]
[[Category: Ribosomal protein]]
[[Category: Schwalbe H]]
[[Category: Ribosomal protein s1 domain 3 and domain 4 vibrio vulnificus ob-fold mrna binding rs1-d34]]

Latest revision as of 14:09, 14 June 2023

NMR structure of D3-D4 domains of Vibrio vulnificus ribosomal protein S1NMR structure of D3-D4 domains of Vibrio vulnificus ribosomal protein S1

Structural highlights

7a05 is a 1 chain structure with sequence from Vibrio vulnificus. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

A0A3Q0L6Y6_VIBVU Binds mRNA; thus facilitating recognition of the initiation point. It is needed to translate mRNA with a short Shine-Dalgarno (SD) purine-rich sequence.[PIRNR:PIRNR002111]

Publication Abstract from PubMed

The ribosomal S1 protein (rS1) is indispensable for translation initiation in Gram-negative bacteria. rS1 is a multidomain protein that acts as an RNA chaperone and ensures that mRNAs can bind the ribosome in a single-stranded conformation, which could be related to fast recognition. Although many ribosome structures were solved in recent years, a high-resolution structure of a two-domain mRNA-binding competent rS1 construct is not yet available. Here, we present the NMR solution structure of the minimal mRNA-binding fragment of Vibrio Vulnificus rS1 containing the domains D3 and D4. Both domains are homologues and adapt an oligonucleotide-binding fold (OB fold) motif. NMR titration experiments reveal that recognition of miscellaneous mRNAs occurs via a continuous interaction surface to one side of these structurally linked domains. Using a novel paramagnetic relaxation enhancement (PRE) approach and exploring different spin-labeling positions within RNA, we were able to track the location and determine the orientation of the RNA in the rS1-D34 bound form. Our investigations show that paramagnetically labeled RNAs, spiked into unmodified RNA, can be used as a molecular ruler to provide structural information on protein-RNA complexes. The dynamic interaction occurs on a defined binding groove spanning both domains with identical beta2-beta3-beta5 interfaces. Evidently, the 3'-ends of the cis-acting RNAs are positioned in the direction of the N-terminus of the rS1 protein, thus towards the 30S binding site and adopt a conformation required for translation initiation.

NMR structure of the Vibrio vulnificus ribosomal protein S1 domains D3 and D4 provides insights into molecular recognition of single-stranded RNAs.,Qureshi NS, Matzel T, Cetiner EC, Schnieders R, Jonker HRA, Schwalbe H, Furtig B Nucleic Acids Res. 2021 Jul 5. pii: 6315300. doi: 10.1093/nar/gkab562. PMID:34223902[1]

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

See Also

References

  1. Qureshi NS, Matzel T, Cetiner EC, Schnieders R, Jonker HRA, Schwalbe H, Furtig B. NMR structure of the Vibrio vulnificus ribosomal protein S1 domains D3 and D4 provides insights into molecular recognition of single-stranded RNAs. Nucleic Acids Res. 2021 Jul 5. pii: 6315300. doi: 10.1093/nar/gkab562. PMID:34223902 doi:http://dx.doi.org/10.1093/nar/gkab562
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