4N0A

Crystal structure of Lsm2-3-Pat1C complex from Saccharomyces cerevisiae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.272 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Lsm2 and Lsm3 bridge the interaction of the Lsm1-7 complex with Pat1 for decapping activation

Wu, D.Muhlrad, D.Bowler, M.W.Jiang, S.Liu, Z.Parker, R.Song, H.

(2014) Cell Res. 24: 233-246

  • DOI: 10.1038/cr.2013.152

  • PubMed Abstract: 
  • The evolutionarily conserved Lsm1-7-Pat1 complex is the most critical activator of mRNA decapping in eukaryotic cells and plays many roles in normal decay, AU-rich element-mediated decay, and miRNA silencing, yet how Pat1 interacts with the Lsm1-7 co ...

    The evolutionarily conserved Lsm1-7-Pat1 complex is the most critical activator of mRNA decapping in eukaryotic cells and plays many roles in normal decay, AU-rich element-mediated decay, and miRNA silencing, yet how Pat1 interacts with the Lsm1-7 complex is unknown. Here, we show that Lsm2 and Lsm3 bridge the interaction between the C-terminus of Pat1 (Pat1C) and the Lsm1-7 complex. The Lsm2-3-Pat1C complex and the Lsm1-7-Pat1C complex stimulate decapping in vitro to a similar extent and exhibit similar RNA-binding preference. The crystal structure of the Lsm2-3-Pat1C complex shows that Pat1C binds to Lsm2-3 to form an asymmetric complex with three Pat1C molecules surrounding a heptameric ring formed by Lsm2-3. Structure-based mutagenesis revealed the importance of Lsm2-3-Pat1C interactions in decapping activation in vivo. Based on the structure of Lsm2-3-Pat1C, a model of Lsm1-7-Pat1 complex is constructed and how RNA binds to this complex is discussed.


    Organizational Affiliation

    Department of Biochemistry and Howard Hughes Medical Institute, University of Colorado, Boulder, Boulder CO 80303, USA.,1] Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673 [2] Life Sciences Institute, Zhejiang University, 388 Yuhangtang Road, Hangzhou, Zhejiang 310000, China [3] Department of Biochemistry, National University of Singapore, 14 Science Drive, Singapore 117543.,Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673.,Life Sciences Institute, Zhejiang University, 388 Yuhangtang Road, Hangzhou, Zhejiang 310000, China.,1] European Molecular Biology Laboratory, 6 rue Jules Horowitz, BP 181, 38042, Grenoble, France [2] Unit of Virus Host-Cell Interactions, UJF-EMBL-CNRS, UMI 3265, 6 rue Jules Horowitz, 38042 Grenoble Cedex 9, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm3
A, B, E, F
89Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: LSM3 (SMX4, USS2)
Find proteins for P57743 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: LSM3
Go to UniProtKB:  P57743
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm2
C, D, G
109Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: LSM2 (SMX5, SNP3)
Find proteins for P38203 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: LSM2
Go to UniProtKB:  P38203
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA topoisomerase 2-associated protein PAT1
H, I, J
380Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 1 
Gene Names: PAT1 (MRT1)
Find proteins for P25644 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P25644
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.272 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 138.447α = 90.00
b = 251.511β = 112.09
c = 120.310γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXphasing
PHENIXrefinement
PHENIXmodel building
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-10-01 
  • Released Date: 2013-12-04 
  • Deposition Author(s): Wu, D.H.

Revision History 

  • Version 1.0: 2013-12-04
    Type: Initial release
  • Version 1.1: 2014-01-22
    Type: Database references
  • Version 1.2: 2014-02-19
    Type: Database references