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]]' scene=''> | <StructureSection load='7a05' size='340' side='right'caption='[[7a05]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>Full | <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> | ||
</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> | </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> | ||
<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 == | |||
[[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] | |||
<div style="background-color:#fffaf0;"> | |||
== 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<ref>PMID:34223902</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 7a05" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Atcc 27562]] | |||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Cetiner | [[Category: Cetiner, E C]] | ||
[[Category: Fuertig B]] | [[Category: Fuertig, B]] | ||
[[Category: Jonker | [[Category: Jonker, H R.A]] | ||
[[Category: Matzel T]] | [[Category: Matzel, T]] | ||
[[Category: Qureshi | [[Category: Qureshi, N S]] | ||
[[Category: Schnieders S]] | [[Category: Schnieders, S]] | ||
[[Category: Schwalbe H]] | [[Category: Schwalbe, H]] | ||
[[Category: Ribosomal protein]] | |||
[[Category: Ribosomal protein s1 domain 3 and domain 4 vibrio vulnificus ob-fold mrna binding rs1-d34]] | |||
Revision as of 13:03, 14 July 2021
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
Function[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] Publication Abstract from PubMedThe 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. References
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