PDBsum entry 1b7f

RNA-binding protein/RNA

PDB id: 1b7f

Contents

Protein chains

167 a.a. *

DNA/RNA

Waters ×84

* Residue conservation analysis

PDB id:

1b7f

Name:

RNA-binding protein/RNA

Title:

Sxl-lethal protein/RNA complex

Structure:

RNA (5'-r(p Gp Up Up Gp Up Up Up Up Up Up Up U)-3'). Chain: p, q. Synonym: tra pre-mRNA. Engineered: yes. Protein (sxl-lethal protein). Chain: a, b. Fragment: 2 rnp-domains. Engineered: yes. Mutation: yes

Source:

Synthetic: yes. Other_details: origin of the sequence: drosophila melanogaster, nucleus. Drosophila melanogaster. Fruit fly. Organism_taxid: 7227. Cellular_location: nucleus. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PQS)

Resolution:

2.60Å R-factor: 0.201 R-free: 0.294

Authors:

N.Handa,O.Nureki,K.Kurimoto,I.Kim,H.Sakamoto,Y.Shimura,Y.Muto, S.Yokoyama,Riken Structural Genomics/proteomics Initiative (Rsgi)

Key ref:

N.Handa et al. (1999). Structural basis for recognition of the tra mRNA precursor by the Sex-lethal protein. Nature, 398, 579-585. PubMed id: 10217141 DOI: 10.1038/19242

Date:

23-Jan-99 Release date: 03-May-99

Protein chains

P19339  (SXL_DROME) -  Protein sex-lethal from Drosophila melanogaster

Seq: 354 a.a.

Struc: 167 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DNA/RNA chains

G-U-U-G-U-U-U-U-U-U-U-U 12 bases

G-U-U-G-U-U-U-U-U-U-U-U 12 bases

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1038/19242

Nature 398:579-585 (1999)

PubMed id: 10217141

Structural basis for recognition of the tra mRNA precursor by the Sex-lethal protein.

N.Handa, O.Nureki, K.Kurimoto, I.Kim, H.Sakamoto, Y.Shimura, Y.Muto, S.Yokoyama.

ABSTRACT

The Sex-lethal (Sxl) protein of Drosophila melanogaster regulates alternative splicing of the transformer (tra) messenger RNA precursor by binding to the tra polypyrimidine tract during the sex-determination process. The crystal structure has now been determined at 2.6 A resolution of the complex formed between two tandemly arranged RNA-binding domains of the Sxl protein and a 12-nucleotide, single-stranded RNA derived from the tra polypyrimidine tract. The two RNA-binding domains have their beta-sheet platforms facing each other to form a V-shaped cleft. The RNA is characteristically extended and bound in this cleft, where the UGUUUUUUU sequence is specifically recognized by the protein. This structure offers the first insight, to our knowledge, into how a protein binds specifically to a cognate RNA without any intramolecular base-pairing.

Selected figure(s)

Figure 3.
Figure 3: Distribution of the electrostatic potential on the solvent-accessible surface of Sxl (stereo view). The bound 12-nucleotide RNA is indicated in yellow by a ball-and-stick representation. The V-shaped interdomain cleft and the surface on the RBD2 -sheet platform are strongly electropositive (blue); these accommodate the phosphodiester backbone of the elongated RNA well. On the other hand, electronegative regions (red) are scattered. This figure was drawn using MOLMOL^50.

Figure 4.
Figure 4: The U3–U11 (UGUUUUUUU) RNA segment in the complex (stereo view). RNA is represented by a wire-loop model in yellow, with atoms of nitrogen, oxygen and phosphorus shown in blue, red and purple, respectively. The ribose moieties, except for U8, are in the C2'-endo form. Light green broken lines show the intramolecular hydrogen bonds that characterize the turn conformation of RNA. The side chains of the amino acids that interact with the RNA backbone are represented in green. Red broken lines denote the intermolecular hydrogen bonds of the amino-acid side chains with the phosphate–sugar backbone.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (1999, 398, 579-585) copyright 1999.

Figures were selected by an automated process.