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5o1x

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Structure of Nrd1 RNA binding domain

Structural highlights

5o1x is a 1 chain structure with sequence from Saccharomyces cerevisiae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.6Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NRD1_YEAST Plays a role in sequence-specific regulation of nuclear pre-mRNA abundance.

Publication Abstract from PubMed

Transcription termination of non-coding RNAs is regulated in yeast by a complex of three RNA binding proteins: Nrd1, Nab3 and Sen1. Nrd1 is central in this process by interacting with Rbp1 of RNA polymerase II, Trf4 of TRAMP and GUAA/G terminator sequences. We lack structural data for the last of these binding events. We determined the structures of Nrd1 RNA binding domain and its complexes with three GUAA-containing RNAs, characterized RNA binding energetics and tested rationally designed mutants in vivo. The Nrd1 structure shows an RRM domain fused with a second alpha/beta domain that we name split domain (SD), because it is formed by two non-consecutive segments at each side of the RRM. The GUAA interacts with both domains and with a pocket of water molecules, trapped between the two stacking adenines and the SD. Comprehensive binding studies demonstrate for the first time that Nrd1 has a slight preference for GUAA over GUAG and genetic and functional studies suggest that Nrd1 RNA binding domain might play further roles in non-coding RNAs transcription termination.

The structure of transcription termination factor Nrd1 reveals an original mode for GUAA recognition.,Franco-Echevarria E, Gonzalez-Polo N, Zorrilla S, Martinez-Lumbreras S, Santiveri CM, Campos-Olivas R, Sanchez M, Calvo O, Gonzalez B, Perez-Canadillas JM Nucleic Acids Res. 2017 Sep 29;45(17):10293-10305. doi: 10.1093/nar/gkx685. PMID:28973465^[1]

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

References

↑ Franco-Echevarria E, Gonzalez-Polo N, Zorrilla S, Martinez-Lumbreras S, Santiveri CM, Campos-Olivas R, Sanchez M, Calvo O, Gonzalez B, Perez-Canadillas JM. The structure of transcription termination factor Nrd1 reveals an original mode for GUAA recognition. Nucleic Acids Res. 2017 Sep 29;45(17):10293-10305. doi: 10.1093/nar/gkx685. PMID:28973465 doi:http://dx.doi.org/10.1093/nar/gkx685

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5o1x"

Categories: Large Structures | Saccharomyces cerevisiae | Franco-Echevarria E | Gonzalez B | Perez-Canadillas JM

@@ Line 1: / Line 1: @@
 ==Structure of Nrd1 RNA binding domain==
-<StructureSection load='5o1x' size='340' side='right' caption='[[5o1x]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
+<StructureSection load='5o1x' size='340' side='right'caption='[[5o1x]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5o1x]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O1X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5O1X FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5o1x]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O1X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5O1X FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</scene></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]] 1.6&#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=5o1x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o1x OCA], [http://pdbe.org/5o1x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5o1x RCSB], [http://www.ebi.ac.uk/pdbsum/5o1x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5o1x ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</scene></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=5o1x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o1x OCA], [https://pdbe.org/5o1x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5o1x RCSB], [https://www.ebi.ac.uk/pdbsum/5o1x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5o1x ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/NRD1_YEAST NRD1_YEAST]] Plays a role in sequence-specific regulation of nuclear pre-mRNA abundance.
+[https://www.uniprot.org/uniprot/NRD1_YEAST NRD1_YEAST] Plays a role in sequence-specific regulation of nuclear pre-mRNA abundance.
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Franco-Echevarria, E]]
+[[Category: Large Structures]]
-[[Category: Gonzalez, B]]
+[[Category: Saccharomyces cerevisiae]]
-[[Category: Perez-Canadillas, J M]]
+[[Category: Franco-Echevarria E]]
-[[Category: Nrd1]]
+[[Category: Gonzalez B]]
-[[Category: Nrd1 complex]]
+[[Category: Perez-Canadillas JM]]
-[[Category: Rna-binding]]
-[[Category: Rrm]]
-[[Category: Transcription]]
-[[Category: Transcription non-coding rna]]

5o1x

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Current revision

Structure of Nrd1 RNA binding domain

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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