5O1Z

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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, C.M.Campos-Olivas, R.Sanchez, M.Calvo, O.Gonzalez, B.Perez-Canadillas, J.M.

(2017) Nucleic Acids Res. 45: 10293-10305

  • DOI: 10.1093/nar/gkx685
  • Primary Citation of Related Structures:  5O1T, 5O1W, 5O1X, 5O1Y, 5O20

  • 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 seq ...

    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.


    Organizational Affiliation

    Departament of Crystallography and Structural Biology, Institute of Physical-Chemistry "Rocasolano", CSIC, C/ Serrano 119, 28006 Madrid, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein NRD1
A
180Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: NRD1
Find proteins for P53617 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P53617
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(*CP*GP*UP*AP*AP*A)-3')B6Saccharomyces cerevisiae
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.181 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 64.529α = 90.00
b = 64.529β = 90.00
c = 157.033γ = 90.00
Software Package:
Software NamePurpose
Cootmodel building
XDSdata reduction
Aimlessdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
CSICSpainBFU2014-53762-P, CTQ2014-52633

Revision History 

  • Version 1.0: 2017-08-02
    Type: Initial release
  • Version 1.1: 2017-09-13
    Type: Structure summary
  • Version 1.2: 2017-10-11
    Type: Database references