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.

5o1x

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

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 3: / Line 3: @@
 <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://proteopedia.org/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" id="ligandDat"><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://proteopedia.org/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 23: / Line 24: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Franco-Echevarria, E]]
+[[Category: Saccharomyces cerevisiae]]
-[[Category: Gonzalez, B]]
+[[Category: Franco-Echevarria E]]
-[[Category: Perez-Canadillas, J M]]
+[[Category: Gonzalez B]]
-[[Category: Nrd1]]
+[[Category: Perez-Canadillas JM]]
-[[Category: Nrd1 complex]]
-[[Category: Rna-binding]]
-[[Category: Rrm]]
-[[Category: Transcription]]
-[[Category: Transcription non-coding rna]]

5o1x

From Proteopedia

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?)

Views

Personal tools

Navigation

Search

Toolbox