4M78

Crystal structure of Lsm2-8 complex, space group P21


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.794 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.254 

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
  • Primary Citation of Related Structures:  4M75, 4M77, 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 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 [3].




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm8
A, H
96Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: LSM8
Find proteins for P47093 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: LSM8
Go to UniProtKB:  P47093
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm2
B, I
95Saccharomyces cerevisiae (strain ATCC 204508 / S288c)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, J
89Saccharomyces cerevisiae (strain ATCC 204508 / S288c)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 LSm6
D, K
86Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: LSM6
Find proteins for Q06406 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: LSM6
Go to UniProtKB:  Q06406
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm5
E, L
93Saccharomyces cerevisiae (strain ATCC 204508 / S288c)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 LSm7
F, M
115Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: LSM7
Find proteins for P53905 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: LSM7
Go to UniProtKB:  P53905
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm4
G, N
93Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: LSM4 (SDB23, USS1)
Find proteins for P40070 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: LSM4
Go to UniProtKB:  P40070
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.794 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.254 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 79.721α = 90.00
b = 76.638β = 97.00
c = 113.554γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
ADSCdata collection
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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