4C92

Crystal structure of the yeast Lsm1-7 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.299 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.211 

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:  

  • 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 bi ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SM-LIKE PROTEIN LSM1
A
146Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: LSM1 (SPB8)
Find proteins for P47017 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: LSM1
Go to UniProtKB:  P47017
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM2
B
105Saccharomyces 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
U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM3
C
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: 4
MoleculeChainsSequence LengthOrganismDetails
U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM4
D
114Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: LSM4 (SDB23, USS1)
Find proteins for P40070 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: LSM4
Go to UniProtKB:  P40070
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM5
E
93Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: LSM5
Find proteins for P40089 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: LSM5
Go to UniProtKB:  P40089
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM6
F
86Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: LSM6
Find proteins for Q06406 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: LSM6
Go to UniProtKB:  Q06406
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM7
G
115Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: LSM7
Find proteins for P53905 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: LSM7
Go to UniProtKB:  P53905
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.299 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.211 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 61.796α = 90.00
b = 90.570β = 100.80
c = 68.462γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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

Revision History 

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