4M78

Crystal structure of Lsm2-8 complex, space group P21


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.256 

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This is version 1.3 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: https://doi.org/10.1038/nature12803
  • Primary Citation of Related Structures:  
    4M75, 4M77, 4M78, 4M7A, 4M7D

  • 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 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 [3].


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm8
A, H
96Saccharomyces cerevisiae S288CMutation(s): 4 
Gene Names: LSM8YJR022WJ1464YJR83.16
UniProt
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UniProt GroupP47093
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm2
B, I
95Saccharomyces cerevisiae S288CMutation(s): 1 
Gene Names: LSM2SMX5SNP3YBL026WYBL0425
UniProt
Find proteins for P38203 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm3
C, J
89Saccharomyces cerevisiae S288CMutation(s): 2 
Gene Names: LSM3SMX4USS2YLR438C-A
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm6
D, K
86Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LSM6YDR378CD9481.18
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm5
E, L
93Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LSM5YER146W
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm7
F, M
115Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LSM7YNL147WN1202N1780
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm4
G, N
93Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LSM4SDB23USS1YER112W
UniProt
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.256 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.721α = 90
b = 76.638β = 97
c = 113.554γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Refinement description