Crystal structure of a heptameric ring complex of yeast SmF in spacegroup P4122

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.254 

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Homomeric ring assemblies of eukaryotic Sm proteins have affinity for both RNA and DNA: Crystal structure of an oligomeric complex of yeast SmF

Collins, B.M.Cubeddu, L.Naidoo, N.Harrop, S.J.Kornfeld, G.D.Dawes, I.W.Curmi, P.M.G.Mabbutt, B.C.

(2003) J Biol Chem 278: 17291-17298

  • DOI: https://doi.org/10.1074/jbc.M211826200
  • Primary Citation of Related Structures:  
    1N9R, 1N9S

  • PubMed Abstract: 

    Sm and Sm-like proteins are key components of small ribonucleoproteins involved in many RNA and DNA processing pathways. In eukaryotes, these complexes contain seven unique Sm or Sm-like (Lsm) proteins assembled as hetero-heptameric rings, whereas in Archaea and bacteria six or seven-membered rings are made from only a single polypeptide chain. Here we show that single Sm and Lsm proteins from yeast also have the capacity to assemble into homo-oligomeric rings. Formation of homo-oligomers by the spliceosomal small nuclear ribonucleoprotein components SmE and SmF preclude hetero-interactions vital to formation of functional small nuclear RNP complexes in vivo. To better understand these unusual complexes, we have determined the crystal structure of the homomeric assembly of the spliceosomal protein SmF. Like its archaeal/bacterial homologs, the SmF complex forms a homomeric ring but in an entirely novel arrangement whereby two heptameric rings form a co-axially stacked dimer via interactions mediated by the variable loops of the individual SmF protein chains. Furthermore, we demonstrate that the homomeric assemblies of yeast Sm and Lsm proteins are capable of binding not only to oligo(U) RNA but, in the case of SmF, also to oligo(dT) single-stranded DNA.

  • Organizational Affiliation

    Cambridge Institute for Medical Research, University of Cambridge, Department of Clinical Biochemistry, Hills Road, Cambridge CB2 2XY, United Kingdom.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein F
A, B, C, D, E
A, B, C, D, E, F, G
93Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P54999 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P54999 
Go to UniProtKB:  P54999
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54999
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.254 
  • Space Group: P 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.891α = 90
b = 79.891β = 90
c = 251.188γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-12-13
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2023-08-16
    Changes: Data collection, Database references, Refinement description