PDBsum entry 2et3

RNA

PDB id: 2et3

Contents

DNA/RNA

Ligands

LLL ×2

Waters ×8

PDB id:

2et3

Name:

RNA

Title:

Complex between gentamicin c1a and the 16s-rrna a-site

Structure:

5'-r( Cp Gp Cp Gp Up Cp Ap Cp Ap Cp Cp Gp Gp Up Gp Ap Ap Gp Up Cp Gp C)-3'. Chain: a, b. Engineered: yes

Source:

Synthetic: yes

Biol. unit:

Dimer (from PQS)

Resolution:

2.80Å R-factor: 0.210 R-free: 0.251

Authors:

E.Westhof

Key ref:

B.François et al. (2005). Crystal structures of complexes between aminoglycosides and decoding A site oligonucleotides: role of the number of rings and positive charges in the specific binding leading to miscoding. Nucleic Acids Res, 33, 5677-5690. PubMed id: 16214802

Date:

27-Oct-05 Release date: 13-Dec-05

DNA/RNA chains

G-C-G-U-C-A-C-A-C-C-G-G-U-G-A-A-G-U-C-G-C 21 bases

G-C-G-U-C-A-C-A-C-C-G-G-U-G-A-A-G-U-C-G-C 21 bases

Nucleic Acids Res 33:5677-5690 (2005)

PubMed id: 16214802

Crystal structures of complexes between aminoglycosides and decoding A site oligonucleotides: role of the number of rings and positive charges in the specific binding leading to miscoding.

B.François, R.J.Russell, J.B.Murray, F.Aboul-ela, B.Masquida, Q.Vicens, E.Westhof.

ABSTRACT

The crystal structures of six complexes between aminoglycoside antibiotics (neamine, gentamicin C1A, kanamycin A, ribostamycin, lividomycin A and neomycin B) and oligonucleotides containing the decoding A site of bacterial ribosomes are reported at resolutions between 2.2 and 3.0 A. Although the number of contacts between the RNA and the aminoglycosides varies between 20 and 31, up to eight direct hydrogen bonds between rings I and II of the neamine moiety are conserved in the observed complexes. The puckered sugar ring I is inserted into the A site helix by stacking against G1491 and forms a pseudo base pair with two H-bonds to the Watson-Crick sites of the universally conserved A1408. This central interaction helps to maintain A1492 and A1493 in a bulged-out conformation. All these structures of the minimal A site RNA complexed to various aminoglycosides display crystal packings with intermolecular contacts between the bulging A1492 and A1493 and the shallow/minor groove of Watson-Crick pairs in a neighbouring helix. In one crystal, one empty A site is observed. In two crystals, two aminoglycosides are bound to the same A site with one bound specifically and the other bound in various ways in the deep/major groove at the edge of the A sites.