This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


2mf0

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (07:00, 1 May 2024) (edit) (undo)
 
(2 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Large structure}}
+
 
==Structural basis of the non-coding RNA RsmZ acting as protein sponge: Conformer L of RsmZ(1-72)/RsmE(dimer) 1to3 complex==
==Structural basis of the non-coding RNA RsmZ acting as protein sponge: Conformer L of RsmZ(1-72)/RsmE(dimer) 1to3 complex==
-
<StructureSection load='2mf0' size='340' side='right' caption='[[2mf0]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
+
<StructureSection load='2mf0' size='340' side='right'caption='[[2mf0]]' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[2mf0]] is a 7 chain structure with sequence from [http://en.wikipedia.org/wiki/Psef5 Psef5]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2MF0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2MF0 FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[2mf0]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_fluorescens Pseudomonas fluorescens] and [https://en.wikipedia.org/wiki/Pseudomonas_protegens_Pf-5 Pseudomonas protegens Pf-5]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2MF0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2MF0 FirstGlance]. <br>
-
</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2mf1|2mf1]]</td></tr>
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
-
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rsmE, csrA, PFL_2095 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=220664 PSEF5])</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=2mf0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2mf0 OCA], [https://pdbe.org/2mf0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2mf0 RCSB], [https://www.ebi.ac.uk/pdbsum/2mf0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2mf0 ProSAT]</span></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=2mf0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2mf0 OCA], [http://pdbe.org/2mf0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2mf0 RCSB], [http://www.ebi.ac.uk/pdbsum/2mf0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2mf0 ProSAT]</span></td></tr>
+
</table>
</table>
-
{{Large structure}}
 
== Function ==
== Function ==
-
[[http://www.uniprot.org/uniprot/Q4KEY0_PSEF5 Q4KEY0_PSEF5]] Could accelerate the degradation of some genes transcripts potentially through selective RNA binding (By similarity).[HAMAP-Rule:MF_00167][SAAS:SAAS003751_004_007709]
+
[https://www.uniprot.org/uniprot/CSRA1_PSEPH CSRA1_PSEPH] A translational regulator that binds mRNA to regulate translation initiation and/or mRNA stability (PubMed:17704818, PubMed:23635605). Post-transcriptionally represses the expression of genes controlled by GacA/GacS (PubMed:15601712, PubMed:23635605). Binds the 5' UTR of mRNA; the mRNA binds to the outside edge to each monomer and each dimer could bind the same mRNA twice (PubMed:17704818). Recognizes a (A/U)CANGGANG(U/A) consensus, binds to GGA (part of the Shine-Dalgarno sequence) in the 5' UTR loop, which prevents ribosome binding (PubMed:17704818, PubMed:24561806, PubMed:23635605). Overexpression represses target protein expression; mutating nucleotides in the 5' UTR abolishes repression in vivo (PubMed:17704818, PubMed:23635605). Binds specifically to small RNAs (sRNA) RsmX, RsmZ and RsmY; these sRNAs fold into secondary structures with multiple GGA sequences in loops to which the CsrA proteins bind (PubMed:15601712, PubMed:16286659, PubMed:24828038). Binding to RsmX, RsmY or RsmZ titrates the protein so that it can no longer bind mRNA and repress translation (PubMed:15601712, PubMed:24828038). RsmZ can bind up to 5 CsrA1 (rsmE) dimers; they bind cooperatively to GGA sequences in RsmZ in a defined order (PubMed:24828038, PubMed:24561806). Required for optimal expression and stability of sRNAs RsmX, RsmY and RsmZ (PubMed:15601712, PubMed:16286659). Four CsrA1 dimers maximally protect RsmZ from RNase activity (PubMed:24828038). Deletion of rsmX, rsmY or rsmZ alone has no detectable phenotype, but a double rsmY-rsmZ deletion has a marked decrease in production of secondary metabolites HCN, exoprotease AprA, antifungal agent 2,4-diacetylphloroglucinol and swarming motility, and protects cucumber plants from fungal infection less well than wild-type; the triple sRNA deletion has even stronger loss of these phenotypes (PubMed:16286659).<ref>PMID:15601712</ref> <ref>PMID:16286659</ref> <ref>PMID:17704818</ref> <ref>PMID:23635605</ref> <ref>PMID:24561806</ref> <ref>PMID:24828038</ref>
-
<div style="background-color:#fffaf0;">
+
-
== Publication Abstract from PubMed ==
+
-
MicroRNA and protein sequestration by non-coding RNAs (ncRNAs) has recently generated much interest. In the bacterial Csr/Rsm system, which is considered to be the most general global post-transcriptional regulatory system responsible for bacterial virulence, ncRNAs such as CsrB or RsmZ activate translation initiation by sequestering homodimeric CsrA-type proteins from the ribosome-binding site of a subset of messenger RNAs. However, the mechanism of ncRNA-mediated protein sequestration is not understood at the molecular level. Here we show for Pseudomonas fluorescens that RsmE protein dimers assemble sequentially, specifically and cooperatively onto the ncRNA RsmZ within a narrow affinity range. This assembly yields two different native ribonucleoprotein structures. Using a powerful combination of nuclear magnetic resonance and electron paramagnetic resonance spectroscopy we elucidate these 70-kilodalton solution structures, thereby revealing the molecular mechanism of the sequestration process and how RsmE binding protects the ncRNA from RNase E degradation. Overall, our findings suggest that RsmZ is well-tuned to sequester, store and release RsmE and therefore can be viewed as an ideal protein 'sponge'.
+
-
 
+
-
Structural basis of the non-coding RNA RsmZ acting as a protein sponge.,Duss O, Michel E, Yulikov M, Schubert M, Jeschke G, Allain FH Nature. 2014 May 29;509(7502):588-92. doi: 10.1038/nature13271. Epub 2014 May 14. PMID:24828038<ref>PMID:24828038</ref>
+
-
 
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
<div class="pdbe-citations 2mf0" style="background-color:#fffaf0;"></div>
+
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Psef5]]
+
[[Category: Large Structures]]
-
[[Category: Allain, F H.T]]
+
[[Category: Pseudomonas fluorescens]]
-
[[Category: Duss, O]]
+
[[Category: Pseudomonas protegens Pf-5]]
-
[[Category: Jeschke, G]]
+
[[Category: Allain FH-T]]
-
[[Category: Michel, E]]
+
[[Category: Duss O]]
-
[[Category: Schubert, M]]
+
[[Category: Jeschke G]]
-
[[Category: Yulikov, M]]
+
[[Category: Michel E]]
-
[[Category: Cooperativity]]
+
[[Category: Schubert M]]
-
[[Category: Electron paramagnetic resonance]]
+
[[Category: Yulikov M]]
-
[[Category: Homo-dimeric protein]]
+
-
[[Category: Large solution structure]]
+
-
[[Category: Messenger rna]]
+
-
[[Category: Multiple protein binding site]]
+
-
[[Category: Non-coding rna]]
+
-
[[Category: Protein sequestration]]
+
-
[[Category: Protein sponge]]
+
-
[[Category: Protein/rna]]
+
-
[[Category: Pseudomonas aeruginosa]]
+
-
[[Category: Ribosome binding site]]
+
-
[[Category: Rna binding protein-rna complex]]
+
-
[[Category: Rnase e cleave site]]
+
-
[[Category: Rnp assembly]]
+
-
[[Category: Translation activation]]
+
-
[[Category: Translation repressor protein]]
+
-
[[Category: Two conformation]]
+

Current revision

Structural basis of the non-coding RNA RsmZ acting as protein sponge: Conformer L of RsmZ(1-72)/RsmE(dimer) 1to3 complex

PDB ID 2mf0

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2mf0"
Personal tools