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



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 

  • DOI: 10.1261/rna.075879.120
  • Structures With Same Primary Citation

  • 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 cytoplasmi ...

    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 C-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

    University of Wisconsin, Madison butcher@biochem.wisc.edu.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm1
A
86Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: lsm1SPBC3D6.08c
Find proteins for P87173 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  P87173
Protein Feature View
  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm2
B
96Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: lsm2SPCC1620.01c
Find proteins for O94408 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  O94408
Protein Feature View
  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Probable U6 snRNA-associated Sm-like protein LSm3
C
95Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: lsm3SPBC9B6.05c
Find proteins for Q9Y7M4 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  Q9Y7M4
Protein Feature View
  • Reference Sequence

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Probable U6 snRNA-associated Sm-like protein LSm4
D
129Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: lsm4SPBC30D10.06
Find proteins for O14352 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  O14352
Protein Feature View
  • Reference Sequence

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm5
E
80Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: lsm5SPBC20F10.09
Find proteins for O42978 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  O42978
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  • Reference Sequence

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm6
F
77Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: lsm6SPAC2F3.17c
Find proteins for Q9UUI1 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  Q9UUI1
Protein Feature View
  • Reference Sequence

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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm7
G
113Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: lsm7SPCC285.12
Find proteins for O74499 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  O74499
Protein Feature View
  • Reference Sequence
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 8
MoleculeChainsLengthOrganism
RNA (5'-R(*AP*UP*UP*UP*UP*G)-3')H6synthetic construct
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

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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 

  • Version 1.0: 2020-06-17
    Type: Initial release