6O3X

Crystal structure of yeast Nrd1 CID in complex with Sen1 NIM2

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history. 


Literature

Identification of Three Sequence Motifs in the Transcription Termination Factor Sen1 that Mediate Direct Interactions with Nrd1.

Zhang, Y., Chun, Y., Buratowski, S., Tong, L.

(2019) Structure 27: 1156-1161.e4

  • DOI: https://doi.org/10.1016/j.str.2019.04.005
  • Primary Citation of Related Structures:  
    6O3W, 6O3X, 6O3Y

  • PubMed Abstract: 

    The Nrd1-Nab3-Sen1 (NNS) complex carries out the transcription termination of non-coding RNAs (ncRNAs) by RNA polymerase II (Pol II) in yeast, although the detailed interactions among its subunits remain obscure. Here we have identified three sequence motifs in Sen1 that mediate direct interactions with the Pol II CTD interaction domain (CID) of Nrd1, determined the crystal structures of these Nrd1 interaction motifs (NIMs) bound to the CID, and characterized the interactions in vitro and in yeast. Removal of all three NIMs abolishes NNS complex formation and gives rise to ncRNA termination defects.

    • Organizational Affiliation: 

    Department of Biological Sciences, Columbia University, New York, NY 10027, USA.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein NRD1
A, B, C
172Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: NRD1, YNL251C, N0868
UniProt
Find proteins for P53617 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53617 
Go to UniProtKB:  P53617
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53617
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Helicase SEN1
D, E, F
12Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.6.4
UniProt
Find proteins for Q00416 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q00416 
Go to UniProtKB:  Q00416
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00416
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.69α = 90
b = 102.4β = 90
c = 115.36γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesR35GM118093
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesS10OD012018

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-05
    Type: Initial release
  • Version 1.1: 2019-07-17
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description