PDBsum entry: 1h64

Sm-like protein

PDB id: 1h64

Contents

Protein chains

(+ 22 more) 71 a.a. *

Waters ×1341

* Residue conservation analysis

PDB id:

1h64

Name:

Sm-like protein

Title:

Crystal structure of the sm-related protein of p. Abyssi the biological unit is a heptamer

Structure:

Snrnp sm-like protein. Chain: a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x, y, z, 1, 2. Engineered: yes

Source:

Pyrococcus abyssi. Organism_taxid: 29292. Expressed in: escherichia coli. Expression_system_taxid: 511693. Other_details: genomic DNA

Biol. unit:

Heptamer (from PDB file)

Resolution:

1.9Å R-factor: 0.237 R-free: 0.281

Authors:

C.Mayer,S.Weeks,D.Suck

Key ref:

S.Thore et al. (2003). Crystal structures of the Pyrococcus abyssi Sm core and its complex with RNA. Common features of RNA binding in archaea and eukarya. J Biol Chem, 278, 1239-1247. PubMed id: 12409299 DOI: 10.1074/jbc.M207685200

Date:

05-Jun-01 Release date: 19-Dec-02

Protein chains

Q9V0Y8  (RUXX_PYRAB) -  Putative snRNP Sm-like protein

Seq: 75 a.a.

Struc: 71 a.a.

 Gene Ontology (GO) functional annotation 

• Cellular component: ribonucleoprotein complex (1 term)

DOI no: 10.1074/jbc.M207685200

J Biol Chem 278:1239-1247 (2003)

PubMed id: 12409299

Crystal structures of the Pyrococcus abyssi Sm core and its complex with RNA. Common features of RNA binding in archaea and eukarya.

S.Thore, C.Mayer, C.Sauter, S.Weeks, D.Suck.

ABSTRACT

The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. Their proposed function is to mediate RNA-RNA interactions. We present here the crystal structures of Pyrococcus abyssi Sm protein (PA-Sm1) and its complex with a uridine heptamer. The overall structure of the protein complex, a heptameric ring with a central cavity, is similar to that proposed for the eukaryotic Sm core complex and found for other archaeal Sm proteins. RNA molecules bind to the protein at two different sites. They interact specifically inside the ring with three highly conserved residues, defining the uridine-binding pocket. In addition, nucleotides also interact on the surface formed by the N-terminal alpha-helix as well as a conserved aromatic residue in beta-strand 2 of the PA-Sm1 protein. The mutation of this conserved aromatic residue shows the importance of this second site for the discrimination between RNA sequences. Given the high structural homology between archaeal and eukaryotic Sm proteins, the PA-Sm1.RNA complex provides a model for how the small nuclear RNA contacts the Sm proteins in the Sm core. In addition, it suggests how Sm proteins might exert their function as modulators of RNA-RNA interactions.

Selected figure(s)

Figure 1.
Fig. 1. PA-Sm1 forms a heptameric ring structure, free and in complex with RNA. A, heptamer-heptamer contacts observed in the crystal structure of the free protein. Heptamers interact via the Arg-4 and His-10 residues (highlighted in orange and yellow, respectively) from the N-terminal -helix. B and D, PA-Sm1·U[7] F[o] F[c] difference density map calculated using two PA-Sm1 heptamers and contoured at 2.6 . Densities corresponding to the bound RNA are located between the two rings and within the central cavity. C and E, overall PA-Sm1·U[7] structure. RNA molecules bound to the external sites of the subunits connect the two rings, whereas at the internal uridine-binding pockets, only isolated nucleotides are visible. The calcium ions stabilizing the phosphate groups of the nucleotides in between the two rings are shown in red, protein molecules in ribbon representation are in blue, and RNA molecules are shown in green. Figs. 1-3 were prepared with the programs Setor and Ribbons (54, 55).

Figure 3.
Fig. 3. The RNA nucleotides composing the external binding site. A, binding site for U4 (identical for U1). The nucleotide position and conformation are well defined. Hydrogen bonds are indicated by red dotted lines. Stacking interactions with Tyr-34 stabilizes the uracil base. B, binding site for U5 (and U2). His-10 is kept in a stacking orientation by a hydrogen bond with Tyr-34. 2'-OH group of the ribose of U5 is hydrogen-bonded to Asp-7. C, binding site for U6. Asp-35 and Arg-4 from the neighboring PA-Sm1 subunit are interacting with the base. RNA and protein are depicted in ball and stick representation and colored in green and yellow, respectively.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 1239-1247) copyright 2003.

Figures were selected by an automated process.