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 
  • R-Value Observed: 0.274 

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
  • Primary Citation of Related Structures:  
    4N0A

  • 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 complex is unknown ...

    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

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm3A, B, E, F89Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LSM3SMX4USS2YLR438C-A
UniProt
Find proteins for P57743 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P57743 
Go to UniProtKB:  P57743
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm2C, D, G109Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LSM2SMX5SNP3YBL026WYBL0425
UniProt
Find proteins for P38203 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38203 
Go to UniProtKB:  P38203
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA topoisomerase 2-associated protein PAT1H, I, J380Saccharomyces cerevisiae S288CMutation(s): 1 
Gene Names: MRT1PAT1YCR077CYCR77C
UniProt
Find proteins for P25644 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P25644 
Go to UniProtKB:  P25644
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.272 
  • R-Value Observed: 0.274 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138.447α = 90
b = 251.511β = 112.09
c = 120.31γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
PHENIXmodel building
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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