6PPV

Structure of S. pombe Lsm1-7 with RNA, polyuridine with 3' guanosine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Molecular basis for the distinct cellular functions of the Lsm1-7 and Lsm2-8 complexes.

Montemayor, E.J.Virta, J.M.Hayes, S.M.Nomura, Y.Brow, D.A.Butcher, S.E.

(2020) RNA 26: 1400-1413

  • DOI: 10.1261/rna.075879.120
  • Primary Citation of Related Structures:  
    6PPN, 6PPQ, 6PPP, 6PPV

  • PubMed Abstract: 
  • Eukaryotes possess eight highly conserved Lsm (like Sm) proteins that assemble into circular, heteroheptameric complexes, bind RNA, and direct a diverse range of biological processes. Among the many essential functions of Lsm proteins, the cytoplasmic Lsm1-7 complex initiates mRNA decay, while the nuclear Lsm2-8 complex acts as a chaperone for U6 spliceosomal RNA ...

    Eukaryotes possess eight highly conserved Lsm (like Sm) proteins that assemble into circular, heteroheptameric complexes, bind RNA, and direct a diverse range of biological processes. Among the many essential functions of Lsm proteins, the cytoplasmic Lsm1-7 complex initiates mRNA decay, while the nuclear Lsm2-8 complex acts as a chaperone for U6 spliceosomal RNA. It has been unclear how these complexes perform their distinct functions while differing by only one out of seven subunits. Here, we elucidate the molecular basis for Lsm-RNA recognition and present four high-resolution structures of Lsm complexes bound to RNAs. The structures of Lsm2-8 bound to RNA identify the unique 2',3' cyclic phosphate end of U6 as a prime determinant of specificity. In contrast, the Lsm1-7 complex strongly discriminates against cyclic phosphates and tightly binds to oligouridylate tracts with terminal purines. Lsm5 uniquely recognizes purine bases, explaining its divergent sequence relative to other Lsm subunits. Lsm1-7 loads onto RNA from the 3' end and removal of the Lsm1 carboxy-terminal region allows Lsm1-7 to scan along RNA, suggesting a gated mechanism for accessing internal binding sites. These data reveal the molecular basis for RNA binding by Lsm proteins, a fundamental step in the formation of molecular assemblies that are central to eukaryotic mRNA metabolism.


    Organizational Affiliation

    Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm1A86Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: lsm1SPBC3D6.08c
UniProt
Find proteins for P87173 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm2B96Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: lsm2SPCC1620.01c
UniProt
Find proteins for O94408 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Probable U6 snRNA-associated Sm-like protein LSm3C95Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: lsm3SPBC9B6.05c
UniProt
Find proteins for Q9Y7M4 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Probable U6 snRNA-associated Sm-like protein LSm4D129Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: lsm4SPBC30D10.06
UniProt
Find proteins for O14352 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm5E80Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: lsm5SPBC20F10.09
UniProt
Find proteins for O42978 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm6F77Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: lsm6SPAC2F3.17c
UniProt
Find proteins for Q9UUI1 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm7G113Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: lsm7SPCC285.12
UniProt
Find proteins for O74499 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 8
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(*AP*UP*UP*UP*UP*G)-3')H6synthetic construct
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    • Reference Sequence
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.05 Å
    • R-Value Free: 0.245 
    • R-Value Work: 0.209 
    • R-Value Observed: 0.210 
    • Space Group: P 31 2 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 69.023α = 90
    b = 69.023β = 90
    c = 296.068γ = 120
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    XDSdata reduction
    Aimlessdata scaling
    PHASERphasing

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35 GM118131

    Revision History  (Full details and data files)

    • Version 1.0: 2020-06-17
      Type: Initial release
    • Version 1.1: 2020-09-30
      Changes: Database references