PDBsum entry 1duh

RNA

PDB id: 1duh

Contents

DNA/RNA

Ligands

SO4 ×2

Metals

_LU

_MG

Waters ×6

PDB id:

1duh

Name:

RNA

Title:

Crystal structure of the conserved domain iv of e. Coli 4.5s RNA

Structure:

4.5s RNA domain iv. Chain: a. Fragment: domain iv. Engineered: yes

Source:

Synthetic: yes. Other_details: RNA sequence taken from escherichia coli 4.5s RNA. The RNA was produced by t7 RNA polymerase in vitro transcription using ribozyme technology

Biol. unit:

Dimer (from PDB file)

Resolution:

2.70Å R-factor: 0.230 R-free: 0.245

Authors:

L.Jovine,T.Hainzl,C.Oubridge,W.G.Scott,J.Li,T.K.Sixma,A.Wonacott, T.Skarzynski,K.Nagai

Key ref:

L.Jovine et al. (2000). Crystal structure of the ffh and EF-G binding sites in the conserved domain IV of Escherichia coli 4.5S RNA. Structure, 8, 527-540. PubMed id: 10801497 DOI: 10.1016/S0969-2126(00)00137-4

Date:

17-Jan-00 Release date: 08-May-00

DNA/RNA chain

C-U-C-U-G-U-U-U-A-C-C-A-G-G-U-C-A-G-G-U-C-C-G-G-A-A-G-G-A-A-G-C-A-G-C-C-A-A-G- 45 bases

DOI no: 10.1016/S0969-2126(00)00137-4

Structure 8:527-540 (2000)

PubMed id: 10801497

Crystal structure of the ffh and EF-G binding sites in the conserved domain IV of Escherichia coli 4.5S RNA.

L.Jovine, T.Hainzl, C.Oubridge, W.G.Scott, J.Li, T.K.Sixma, A.Wonacott, T.Skarzynski, K.Nagai.

ABSTRACT

BACKGROUND: Bacterial signal recognition particle (SRP), consisting of 4.5S RNA and Ffh protein, plays an essential role in targeting signal-peptide-containing proteins to the secretory apparatus in the cell membrane. The 4.5S RNA increases the affinity of Ffh for signal peptides and is essential for the interaction between SRP and its receptor, protein FtsY. The 4.5S RNA also interacts with elongation factor G (EF-G) in the ribosome and this interaction is required for efficient translation. RESULTS: We have determined by multiple anomalous dispersion (MAD) with Lu(3+) the 2.7 A crystal structure of a 4.5S RNA fragment containing binding sites for both Ffh and EF-G. This fragment consists of three helices connected by a symmetric and an asymmetric internal loop. In contrast to NMR-derived structures reported previously, the symmetric loop is entirely constituted by non-canonical base pairs. These pairs continuously stack and project unusual sets of hydrogen-bond donors and acceptors into the shallow minor groove. The structure can therefore be regarded as two double helical rods hinged by the asymmetric loop that protrudes from one strand. CONCLUSIONS: Based on our crystal structure and results of chemical protection experiments reported previously, we predicted that Ffh binds to the minor groove of the symmetric loop. An identical decanucleotide sequence is found in the EF-G binding sites of both 4.5S RNA and 23S rRNA. The decanucleotide structure in the 4.5S RNA and the ribosomal protein L11-RNA complex crystals suggests how 4.5S RNA and 23S rRNA might interact with EF-G and function in translating ribosomes.

Selected figure(s)

Figure 2.
Figure 2. Stereo ball-and-stick representation of the symmetric loop A region of the refined 45 RNA crystal structure, with combined, sigmaa-weighted |2F[o]-F[c]| electron-density map contoured at 1.0s.

The above figure is reprinted by permission from Cell Press: Structure (2000, 8, 527-540) copyright 2000.

Figure was selected by an automated process.