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2m23

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NMR solution structure of the d3'-hairpin of the group II intron Sc.ai5gamma including EBS1 bound to IBS1

Structural highlights

2m23 is a 2 chain structure with sequence from Saccharomyces cerevisiae. This structure supersedes the now removed PDB entry 2k64. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Publication Abstract from PubMed

A crucial step of the self-splicing reaction of group II intron ribozymes is the recognition of the 5' exon by the intron. This recognition is achieved by two regions in domain 1 of the intron, the exon-binding sites EBS1 and EBS2 forming base pairs with the intron-binding sites IBS1 and IBS2 located at the end of the 5' exon. The complementarity of the EBS1*IBS1 contact is most important for ensuring site-specific cleavage of the phosphodiester bond between the 5' exon and the intron. Here, we present the NMR solution structures of the d3' hairpin including EBS1 free in solution and bound to the IBS1 7-mer. In the unbound state, EBS1 is part of a flexible 11-nucleotide (nt) loop. Binding of IBS1 restructures and freezes the entire loop region. Mg(2+) ions are bound near the termini of the EBS1*IBS1 helix, stabilizing the interaction. Formation of the 7-bp EBS1*IBS1 helix within a loop of only 11 nt forces the loop backbone to form a sharp turn opposite of the splice site, thereby presenting the scissile phosphate in a position that is structurally unique.

NMR structure of the 5' splice site in the group IIB intron Sc.ai5gamma--conformational requirements for exon-intron recognition.,Kruschel D, Skilandat M, Sigel RK RNA. 2014 Mar;20(3):295-307. doi: 10.1261/rna.041137.113. Epub 2014 Jan 21. PMID:24448450^[1]

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

References

↑ Kruschel D, Skilandat M, Sigel RK. NMR structure of the 5' splice site in the group IIB intron Sc.ai5gamma--conformational requirements for exon-intron recognition. RNA. 2014 Mar;20(3):295-307. doi: 10.1261/rna.041137.113. Epub 2014 Jan 21. PMID:24448450 doi:http://dx.doi.org/10.1261/rna.041137.113

1 Structural highlights
2 Publication Abstract from PubMed
3 See Also
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2m23"

Categories: Large Structures | Saccharomyces cerevisiae | Kruschel D | Sigel RKO | Skilandat M

@@ Line 1: / Line 1: @@
 ==NMR solution structure of the d3'-hairpin of the group II intron Sc.ai5gamma including EBS1 bound to IBS1==
-<StructureSection load='2m23' size='340' side='right'caption='[[2m23]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
+<StructureSection load='2m23' size='340' side='right'caption='[[2m23]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2m23]] is a 2 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2k64 2k64]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2M23 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2M23 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2m23]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2k64 2k64]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2M23 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2M23 FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2k63|2k63]], [[2k64|2k64]], [[2k65|2k65]], [[2k66|2k66]], [[2m1v|2m1v]], [[2m24|2m24]]</div></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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2m23 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2m23 OCA], [https://pdbe.org/2m23 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2m23 RCSB], [https://www.ebi.ac.uk/pdbsum/2m23 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2m23 ProSAT]</span></td></tr>
 </table>
@@ Line 18: / Line 18: @@
 ==See Also==
-*[[Ribozyme|Ribozyme]]
+*[[Ribozyme 3D structures|Ribozyme 3D structures]]
 == References ==
 <references/>
@@ Line 24: / Line 24: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Kruschel, D]]
+[[Category: Saccharomyces cerevisiae]]
-[[Category: Sigel, R K.O]]
+[[Category: Kruschel D]]
-[[Category: Skilandat, M]]
+[[Category: Sigel RKO]]
-[[Category: 5'-splice site]]
+[[Category: Skilandat M]]
-[[Category: Ebs1]]
-[[Category: Group ii intron]]
-[[Category: Hairpin]]
-[[Category: Ibs1]]
-[[Category: Ribozyme]]
-[[Category: Rna]]
-[[Category: Splicing]]

2m23

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Current revision

NMR solution structure of the d3'-hairpin of the group II intron Sc.ai5gamma including EBS1 bound to IBS1

Structural highlights

Publication Abstract from PubMed

See Also

References

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