2L41

Nab3 RRM - UCUU complex


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 60 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Recognition of transcription termination signal by the nuclear polyadenylated RNA-binding (NAB) 3 protein

Hobor, F.Pergoli, R.Kubicek, K.Hrossova, D.Bacikova, V.Zimmermann, M.Pasulka, J.Hofr, C.Vanacova, S.Stefl, R.

(2011) J Biol Chem 286: 3645-3657

  • DOI: 10.1074/jbc.M110.158774
  • Primary Citation of Related Structures:  
    2L41

  • PubMed Abstract: 
  • Non-coding RNA polymerase II transcripts are processed by the poly(A)-independent termination pathway that requires the Nrd1 complex. The Nrd1 complex includes two RNA-binding proteins, the nuclear polyadenylated RNA-binding (Nab) 3 and the nuclear p ...

    Non-coding RNA polymerase II transcripts are processed by the poly(A)-independent termination pathway that requires the Nrd1 complex. The Nrd1 complex includes two RNA-binding proteins, the nuclear polyadenylated RNA-binding (Nab) 3 and the nuclear pre-mRNA down-regulation (Nrd) 1 that bind their specific termination elements. Here we report the solution structure of the RNA-recognition motif (RRM) of Nab3 in complex with a UCUU oligonucleotide, representing the Nab3 termination element. The structure shows that the first three nucleotides of UCUU are accommodated on the β-sheet surface of Nab3 RRM, but reveals a sequence-specific recognition only for the central cytidine and uridine. The specific contacts we identified are important for binding affinity in vitro as well as for yeast viability. Furthermore, we show that both RNA-binding motifs of Nab3 and Nrd1 alone bind their termination elements with a weak affinity. Interestingly, when Nab3 and Nrd1 form a heterodimer, the affinity to RNA is significantly increased due to the cooperative binding. These findings are in accordance with the model of their function in the poly(A) independent termination, in which binding to the combined and/or repetitive termination elements elicits efficient termination.


    Organizational Affiliation

    National Centre for Biomolecular Research, Central European Institute of Technology, Faculty of Science, Masaryk University, Brno CZ-62500, Czechia.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RRM domain from Nuclear polyadenylated RNA-binding protein 3A77Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: NAB3
Find proteins for P38996 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38996 
Go to UniProtKB:  P38996
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(P*UP*CP*UP*U)-3')B4N/A
    Experimental Data & Validation

    Experimental Data

    • Method: SOLUTION NMR
    • Conformers Calculated: 60 
    • Conformers Submitted: 20 
    • Selection Criteria: structures with the lowest energy 
    • OLDERADO: 2L41 Olderado

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2010-11-17
      Type: Initial release
    • Version 1.1: 2011-07-13
      Changes: Version format compliance
    • Version 1.2: 2012-05-30
      Changes: Database references