4EMG | pdb_00004emg

Crystal structure of SpLsm3

• PDB DOI: https://doi.org/10.2210/pdb4EMG/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Schizosaccharomyces pombe 972h-
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-04-12 Released: 2012-06-13 
• Deposition Author(s): Jiang, S.M., Wu, D.H., Song, H.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.277 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.243 (Depositor), 0.243 (DCC) 
• R-Value Observed: 
  0.245 (Depositor) 

Literature

Crystal Structures of Lsm3, Lsm4 and Lsm5/6/7 from Schizosaccharomyces pombe.

Wu, D.H., Jiang, S.M., Bowler, M.W., Song, H.W.

(2012) PLoS One 7: e36768-e36768

• PubMed: 22615807 
• DOI: https://doi.org/10.1371/journal.pone.0036768
• Primary Citation Related Structures: 
  4EMG, 4EMH, 4EMK


• PubMed Abstract: 
  

  Sm-like (Lsm) proteins are ubiquitous and function in many aspects of RNA metabolism, including pre-mRNA splicing, nuclear RNA processing, mRNA decay and miRNA biogenesis. Here three crystal structures including Lsm3, Lsm4 and Lsm5/6/7 sub-complex from S. pombe are reported. These structures show that all the five individual Lsm subunits share a conserved Sm fold, and Lsm3, Lsm4, and Lsm5/6/7 form a heptamer, a trimer and a hexamer within the crystal lattice, respectively. Analytical ultracentrifugation indicates that Lsm3 and Lsm5/6/7 sub-complex exist in solution as a heptamer and a hexamer, respectively while Lsm4 undergoes a dynamic equilibrium between monomer and trimer in solution. RNA binding assays show that Lsm2/3 and Lsm5/6/7 bind to oligo(U) whereas no RNA binding is observed for Lsm3 and Lsm4. Analysis of the inter-subunit interactions in Lsm5/6/7 reveals the organization order among Lsm5, Lsm6 and Lsm7.

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Organizational Affiliation: 
• Institute of Molecular and Cell Biology, Singapore, Singapore.

Biological Assembly 1  

Global Symmetry: Cyclic - C7  (Explore in 3D)
Global Stoichiometry: Homo 7-mer - A7 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C7  (Explore in 3D)
Global Stoichiometry: Homo 7-mer - A7 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 151.49 kDa 
• Atom Count: 8,236 
• Modeled Residue Count: 994 
• Deposited Residue Count: 1,302 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable U6 snRNA-associated Sm-like protein LSm3	A, B, C, D, E, F, G, H, I, J, K, L, M, N	93	Schizosaccharomyces pombe 972h-	Mutation(s): 0  Gene Names: lsm3, SPBC9B6.05c
UniProt
Find proteins for Q9Y7M4 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore Q9Y7M4  Go to UniProtKB:  Q9Y7M4

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D, E, F, G, H, I, J, K, L, M, N	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.277 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.243 (Depositor), 0.243 (DCC) 
• R-Value Observed: 0.245 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.43	α = 90
b = 101.7	β = 90
c = 143.42	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SOLVE	phasing
PHENIX	refinement
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-06-13 
Deposition Author(s): Jiang, S.M., Wu, D.H., Song, H.W.

Revision History  

• Version 1.0: 2012-06-13
  Type: Initial release
  
• Version 1.1: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary