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.

5i9d

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Crystal structure of designed pentatricopeptide repeat protein dPPR-U8A2 in complex with its target RNA U8A2

Structural highlights

5i9d is a 2 chain structure with sequence from Synthetic construct and Unidentified. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.596Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Publication Abstract from PubMed

As a large family of RNA-binding proteins, pentatricopeptide repeat (PPR) proteins mediate multiple aspects of RNA metabolism in eukaryotes. Binding to their target single-stranded RNAs (ssRNAs) in a modular and base-specific fashion, PPR proteins can serve as designable modules for gene manipulation. However, the structural basis for nucleotide-specific recognition by designer PPR (dPPR) proteins remains to be elucidated. Here, we report four crystal structures of dPPR proteins in complex with their respective ssRNA targets. The dPPR repeats are assembled into a right-handed superhelical spiral shell that embraces the ssRNA. Interactions between different PPR codes and RNA bases are observed at the atomic level, revealing the molecular basis for the modular and specific recognition patterns of the RNA bases U, C, A and G. These structures not only provide insights into the functional study of PPR proteins but also open a path towards the potential design of synthetic sequence-specific RNA-binding proteins.

Structural basis for specific single-stranded RNA recognition by designer pentatricopeptide repeat proteins.,Shen C, Zhang D, Guan Z, Liu Y, Yang Z, Yang Y, Wang X, Wang Q, Zhang Q, Fan S, Zou T, Yin P Nat Commun. 2016 Apr 18;7:11285. doi: 10.1038/ncomms11285. PMID:27088764^[1]

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

References

↑ Shen C, Zhang D, Guan Z, Liu Y, Yang Z, Yang Y, Wang X, Wang Q, Zhang Q, Fan S, Zou T, Yin P. Structural basis for specific single-stranded RNA recognition by designer pentatricopeptide repeat proteins. Nat Commun. 2016 Apr 18;7:11285. doi: 10.1038/ncomms11285. PMID:27088764 doi:http://dx.doi.org/10.1038/ncomms11285

1 Structural highlights
2 Publication Abstract from PubMed
3 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5i9d"

@@ Line 3: / Line 3: @@
 <StructureSection load='5i9d' size='340' side='right'caption='[[5i9d]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5i9d]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Miscellaneous_nucleic_acid Miscellaneous nucleic acid]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I9D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5I9D FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5i9d]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct] and [https://en.wikipedia.org/wiki/Unidentified Unidentified]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I9D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5I9D FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5i9f|5i9f]], [[5i9g|5i9g]], [[5i9h|5i9h]]</td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.596&#8491;</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=5i9d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i9d OCA], [http://pdbe.org/5i9d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i9d RCSB], [http://www.ebi.ac.uk/pdbsum/5i9d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5i9d 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=5i9d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i9d OCA], [https://pdbe.org/5i9d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5i9d RCSB], [https://www.ebi.ac.uk/pdbsum/5i9d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5i9d ProSAT]</span></td></tr>
 </table>
 <div style="background-color:#fffaf0;">
@@ Line 21: / Line 21: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Miscellaneous nucleic acid]]
+[[Category: Synthetic construct]]
-[[Category: Guan, Z]]
+[[Category: Unidentified]]
-[[Category: Shen, C]]
+[[Category: Guan Z]]
-[[Category: Yin, P]]
+[[Category: Shen C]]
-[[Category: Zhang, D]]
+[[Category: Yin P]]
-[[Category: Zou, T]]
+[[Category: Zhang D]]
-[[Category: Designer pentatricopeptide repeat protein]]
+[[Category: Zou T]]
-[[Category: Rna binding protein]]
-[[Category: Rna binding protein-rna complex]]
-[[Category: Single-stranded rna]]

5i9d

From Proteopedia

Current revision

Crystal structure of designed pentatricopeptide repeat protein dPPR-U8A2 in complex with its target RNA U8A2

Structural highlights

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox