5O20

Structure of Nrd1 RNA binding domain in complex with RNA (UUAGUAAUCC)

Summary for 5O20

• Entry DOI: 10.2210/pdb5o20/pdb
• Descriptor: Protein NRD1, RNA (5'-R(*UP*AP*GP*UP*AP*AP*UP*C)-3'), 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, ... (4 entities in total)
• Functional Keywords: nrd1, rrm, rna-binding, transcription non-coding rnas, nrd1 complex, transcription
• Biological source: Saccharomyces cerevisiae (Baker's yeast); More
• Cellular location: Nucleus : P53617
• Total number of polymer chains: 2
• Total formula weight: 23353.62

Authors

Franco-Echevarria, E.,Perez-Canadillas, J.M.,Gonzalez, B. (deposition date: 2017-05-19, release date: 2017-08-02, Last modification date: 2024-05-08)

Primary citation

Franco-Echevarria, E.,Gonzalez-Polo, N.,Zorrilla, S.,Martinez-Lumbreras, S.,Santiveri, C.M.,Campos-Olivas, R.,Sanchez, M.,Calvo, O.,Gonzalez, B.,Perez-Canadillas, J.M.
The structure of transcription termination factor Nrd1 reveals an original mode for GUAA recognition.
Nucleic Acids Res., 45:10293-10305, 2017

PubMed Abstract: 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 α/β 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.

PubMed: 28973465
DOI: 10.1093/nar/gkx685

Experimental method

X-RAY DIFFRACTION (3.53 Å)