4C92

Crystal structure of the yeast Lsm1-7 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Architecture of the Lsm1-7-Pat1 Complex: A Conserved Assembly in Eukaryotic Mrna Turnover

Sharif, H.Conti, E.

(2013) Cell Rep 5: 283

  • DOI: 10.1016/j.celrep.2013.10.004
  • Primary Citation of Related Structures:  
    4C8Q, 4C92

  • PubMed Abstract: 
  • The decay of mRNAs is a key step in eukaryotic gene expression. The cytoplasmic Lsm1-7-Pat1 complex is a conserved component of the 5'-to-3' mRNA decay pathway, linking deadenylation to decapping. Lsm1-7 is similar to the nuclear Sm complexes that bind oligo-uridine tracts in snRNAs ...

    The decay of mRNAs is a key step in eukaryotic gene expression. The cytoplasmic Lsm1-7-Pat1 complex is a conserved component of the 5'-to-3' mRNA decay pathway, linking deadenylation to decapping. Lsm1-7 is similar to the nuclear Sm complexes that bind oligo-uridine tracts in snRNAs. The 2.3 Å resolution structure of S. cerevisiae Lsm1-7 shows the presence of a heptameric ring with Lsm1-2-3-6-5-7-4 topology. A distinct structural feature of the cytoplasmic Lsm ring is the C-terminal extension of Lsm1, which plugs the exit site of the central channel and approaches the RNA binding pockets. The 3.7 Å resolution structure of Lsm1-7 bound to the C-terminal domain of Pat1 reveals that Pat1 recognition is not mediated by the distinguishing cytoplasmic subunit, Lsm1, but by Lsm2 and Lsm3. These results show how the auxiliary domains and the canonical Sm folds of the Lsm1-7 complex are organized in order to mediate and modulate macromolecular interactions.


    Organizational Affiliation

    Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SM-LIKE PROTEIN LSM1A146Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P47017 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM2B105Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P38203 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM3C89Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P57743 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM4D114Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P40070 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM5E93Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P40089 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM6F86Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q06406 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM7G115Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P53905 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.796α = 90
b = 90.57β = 100.8
c = 68.462γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2013-10-02 
  • Released Date: 2013-10-16 
  • Deposition Author(s): Sharif, H., Conti, E.

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-16
    Type: Initial release
  • Version 1.1: 2013-10-30
    Changes: Database references
  • Version 1.2: 2013-11-20
    Changes: Database references