6O3Y

Crystal structure of yeast Nrd1 CID in complex with Sen1 NIM3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.799 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.237 

wwPDB Validation 3D Report Full Report


This is version 1.1 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:  

  • 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 sequenc ...

    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.,Department of Biological Sciences, Columbia University, New York, NY 10027, USA. Electronic address: ltong@columbia.edu.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein NRD1
A, B, C
172Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: NRD1
Find proteins for P53617 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P53617
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Helicase SEN1
D, E, F
13Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SEN1
EC: 3.6.4.-
Find proteins for Q00416 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q00416
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.799 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.237 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 98.671α = 90.00
b = 103.046β = 90.00
c = 115.365γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXphasing
XDSdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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 InstituteUnited StatesR35GM118093
National Institutes of Health/National Human Genome Research InstituteUnited StatesS10OD012018

Revision History 

  • Version 1.0: 2019-06-05
    Type: Initial release
  • Version 1.1: 2019-07-17
    Type: Data collection, Database references