4M7A

Crystal structure of Lsm2-8 complex bound to the 3' end sequence of U6 snRNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.246 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structures of the Lsm complex bound to the 3' end sequence of U6 small nuclear RNA.

Zhou, L.Hang, J.Zhou, Y.Wan, R.Lu, G.Yin, P.Yan, C.Shi, Y.

(2014) Nature 506: 116-120

  • DOI: 10.1038/nature12803
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Splicing of precursor messenger RNA (pre-mRNA) in eukaryotic cells is carried out by the spliceosome, which consists of five small nuclear ribonucleoproteins (snRNPs) and a number of accessory factors and enzymes. Each snRNP contains a ring-shaped su ...

    Splicing of precursor messenger RNA (pre-mRNA) in eukaryotic cells is carried out by the spliceosome, which consists of five small nuclear ribonucleoproteins (snRNPs) and a number of accessory factors and enzymes. Each snRNP contains a ring-shaped subcomplex of seven proteins and a specific RNA molecule. The U6 snRNP contains a unique heptameric Lsm protein complex, which specifically recognizes the U6 small nuclear RNA at its 3' end. Here we report the crystal structures of the heptameric Lsm complex, both by itself and in complex with a 3' fragment of U6 snRNA, at 2.8 Å resolution. Each of the seven Lsm proteins interacts with two neighbouring Lsm components to form a doughnut-shaped assembly, with the order Lsm3-2-8-4-7-5-6. The four uridine nucleotides at the 3' end of U6 snRNA are modularly recognized by Lsm3, Lsm2, Lsm8 and Lsm4, with the uracil base specificity conferred by a highly conserved asparagine residue. The uracil base at the extreme 3' end is sandwiched by His 36 and Arg 69 from Lsm3, through π-π and cation-π interactions, respectively. The distinctive end-recognition of U6 snRNA by the Lsm complex contrasts with RNA binding by the Sm complex in the other snRNPs. The structural features and associated biochemical analyses deepen mechanistic understanding of the U6 snRNP function in pre-mRNA splicing.


    Organizational Affiliation

    1] Ministry of Education Key Laboratory of Protein Science, Tsinghua University, Beijing 100084, China [2] Tsinghua-Peking Joint Center for Life Sciences, Center for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm8A, H96Saccharomyces cerevisiae S288CMutation(s): 4 
Gene Names: LSM8YJR022WJ1464YJR83.16
Find proteins for P47093 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P47093
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm2B, I95Saccharomyces cerevisiae S288CMutation(s): 1 
Gene Names: LSM2SMX5SNP3YBL026WYBL0425
Find proteins for P38203 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P38203
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm3C, J89Saccharomyces cerevisiae S288CMutation(s): 2 
Gene Names: LSM3SMX4USS2YLR438C-A
Find proteins for P57743 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P57743
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  • Reference Sequence

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm6D, K86Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LSM6YDR378CD9481.18
Find proteins for Q06406 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm5E, L93Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LSM5YER146W
Find proteins for P40089 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm7F, M115Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LSM7YNL147WN1202N1780
Find proteins for P53905 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm4G, N93Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LSM4SDB23USS1YER112W
Find proteins for P40070 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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  • Reference Sequence
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Entity ID: 8
MoleculeChainsLengthOrganism
U6 snRNAO, P8N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.246 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.624α = 90
b = 78.379β = 100.58
c = 140.565γ = 90
Software Package:
Software NamePurpose
CBASSdata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-11-13
    Type: Initial release
  • Version 1.1: 2013-12-11
    Changes: Database references
  • Version 1.2: 2014-02-19
    Changes: Database references