PDBsum entry: 1n9r

Translation

PDB id: 1n9r

Contents

Protein chains

(+ 1 more) 68 a.a. *

* Residue conservation analysis

PDB id:

1n9r

Name:

Translation

Title:

Crystal structure of a heptameric ring complex of yeast smf spacegroup p4122

Structure:

Small nuclear ribonucleoprotein f. Chain: a, b, c, d, e, f, g. Synonym: smf. Sm-like snrnp protein. Snrnp-f. Sm protein f. Engineered: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

40mer (from PQS)

Resolution:

2.80Å R-factor: 0.254 R-free: 0.268

Authors:

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

Key ref:

B.M.Collins et al. (2003). Homomeric ring assemblies of eukaryotic Sm proteins have affinity for both RNA and DNA. Crystal structure of an oligomeric complex of yeast SmF. J Biol Chem, 278, 17291-17298. PubMed id: 12618433 DOI: 10.1074/jbc.M211826200

Date:

26-Nov-02 Release date: 13-Dec-02

Protein chains

P54999  (RUXF_YEAST) -  Small nuclear ribonucleoprotein F

Seq: 86 a.a.

Struc: 68 a.a.

 Gene Ontology (GO) functional annotation 

• Cellular component: ribonucleoprotein complex (5 terms)
• Biological process: RNA processing (4 terms)
• Biochemical function: molecular_function (3 terms)

DOI no: 10.1074/jbc.M211826200

J Biol Chem 278:17291-17298 (2003)

PubMed id: 12618433

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

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

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.

Selected figure(s)

Figure 1.
Fig. 1. Gel filtration and electrophoresis of recombinant Sm/Lsm proteins. A, gel filtration of Sm/Lsm proteins on a Superdex 75 column in 10 mM Tris (pH 8.0), 200 mM NaCl. (C75S)SmF and Lsm3 appear to form complexes twice the size of (C16S)SmE and the archaeal protein MtLsm which forms a heptameric ring (10). Dimerization of the (C16S)SmE complex is sometimes observed in solution (*). B, silver-stained SDS-PAGE shows samples boiled for 5 min: lane M, 10-kDa marker; lane 1, MtLsm ; lane 2, MtLsm ; lane 3, (C16S)SmE; lane 4, (C75S)SmF; lane 5, Lsm3; and lane 6, Lsm9. C, thermostability of (C16S)SmE and (C75S)SmF homo-oligomers measured from peak areas in gel-filtration traces following 15 min of incubation in a water bath. The SmF complex is resistant to denaturation to 65 °C.

Figure 3.
Fig. 3. Ribbon structures of the SmF homo-oligomeric complex. A, structure of the SmF assembly in the P4[1]22 crystal form. A single SmF subunit is shown at the top. The heptameric ring forms extensive contacts with a symmetry-related heptamer in an identical arrangement to that seen in the P4[3]2[1]2 crystal form. B, two heptameric rings are shown in magenta and green, and residues in the L4 loop that form the interface between the two rings are shown as ball and stick models. C, predicted interactions of Sm/Lsm complexes with nucleic acids and proteins. RNA may pass across one face of the ring (heavy line) or through the central hole (dashed line). We propose that one face of a single ring docks with conserved nucleic acid Sm-binding sequences, whereas the variable loops on the opposite loop L4 face are ideally located for interacting with associated proteins. D, stereo-diagram showing a close-up of the interface between two SmF heptamers (shown in tan and green). The interaction is governed by well ordered contacts between the variable L4 loops of individual SmF chains.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 17291-17298) copyright 2003.

Figures were selected by an automated process.