6O3Y

Crystal structure of yeast Nrd1 CID in complex with Sen1 NIM3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.240 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: 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 ...

    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. Electronic address: ltong@columbia.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein NRD1A, B, C172Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: NRD1YNL251CN0868
UniProt
Find proteins for P53617 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53617 
Go to UniProtKB:  P53617
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Helicase SEN1D, E, F13Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.6.4
UniProt
Find proteins for Q00416 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q00416 
Go to UniProtKB:  Q00416
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download Ideal Coordinates CCD File 
G [auth A], H [auth C]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.240 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.671α = 90
b = 103.046β = 90
c = 115.365γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-02-27 
  • Released Date: 2019-06-05 
  • Deposition Author(s): Zhang, Y., Tong, L.

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