4C8Q

Crystal structure of the yeast Lsm1-7-Pat1 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.251 

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 LSM1A101Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LSM1SPB8YJL124CJ0714
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 cerevisiae S288CMutation(s): 0 
Gene Names: LSM2SMX5SNP3YBL026WYBL0425
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 cerevisiae S288CMutation(s): 0 
Gene Names: LSM3SMX4USS2YLR438C-A
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM4D114Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LSM4SDB23USS1YER112W
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM5E93Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LSM5YER146W
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM6F86Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LSM6YDR378CD9481.18
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM7G115Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LSM7YNL147WN1202N1780
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
DNA TOPOISOMERASE 2-ASSOCIATED PROTEIN PAT1H328Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PAT1MRT1YCR077CYCR77C
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CO
Query on CO

Download Ideal Coordinates CCD File 
I [auth C], J [auth H]COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.251 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 258.687α = 90
b = 258.687β = 90
c = 47.103γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2013-10-01 
  • 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