PDBsum entry 462d

RNA

PDB id: 462d

Contents

DNA/RNA

Metals

_MG ×8

Waters ×240

PDB id:

462d

Name:

RNA

Title:

Crystal structure of the HIV-1 genomic RNA dimerization initiation site

Structure:

RNA (5'- r( Cp Up Up Gp Cp Up Gp Ap Gp Gp Up Gp Cp Ap Cp Ap Cp Ap Gp Cp Ap Ap G) -3'). Chain: a, b. Synonym: HIV-1(mal) genomic RNA dimerization initiation site, dis. Engineered: yes

Source:

Synthetic: yes

Biol. unit:

Dimer (from PQS)

Resolution:

2.30Å R-factor: 0.211 R-free: 0.212

Authors:

E.Ennifar,M.Yusupov,P.Walter,R.Marquet,C.Ehresmann,B.Ehresmann, P.Dumas

Key ref:

E.Ennifar et al. (1999). The crystal structure of the dimerization initiation site of genomic HIV-1 RNA reveals an extended duplex with two adenine bulges. Structure, 7, 1439-1449. PubMed id: 10574792 DOI: 10.1016/S0969-2126(00)80033-7

Date:

18-Mar-99 Release date: 02-Dec-99

DNA/RNA chains

C-U-U-G-C-U-G-A-G-G-U-G-C-A-C-A-C-A-G-C-A-A-G 23 bases

C-U-U-G-C-U-G-A-G-G-U-G-C-A-C-A-C-A-G-C-A-A-G 23 bases

DOI no: 10.1016/S0969-2126(00)80033-7

Structure 7:1439-1449 (1999)

PubMed id: 10574792

The crystal structure of the dimerization initiation site of genomic HIV-1 RNA reveals an extended duplex with two adenine bulges.

E.Ennifar, M.Yusupov, P.Walter, R.Marquet, B.Ehresmann, C.Ehresmann, P.Dumas.

ABSTRACT

BACKGROUND: An important step in retroviral replication is dimerization of the genomic RNA prior to encapsidation. Dimerization is initiated by the formation of a transient 'kissing-loop complex' that is thought to be subsequently matured into an extended duplex by the nucleocapsid protein (NCp). Although chemical probing and nuclear magnetic resonance spectroscopy have provided insight into the structure of the kissing-loop structure, no structural information concerning the extended-duplex state is available so far. RESULTS: The structure of a minimal HIV-1 RNA dimerization initiation site has been solved at 2.3 A resolution in two different space groups. It reveals a 22 base pair extended duplex with two noncanonical Watson-Crick-like G-A mismatches, each adjacent to a bulged-out adenine. The structure shows significant asymmetry in deep groove width and G-A base-pair conformations. A network of eight magnesium cations was clearly identified, one being unusually chelated by the 3' phosphate of each bulge across an extremely narrowed deep major groove. CONCLUSIONS: These crystal structures represent the putative matured form of the initial kissing-loop complex. They show the ability of this self-complementary RNA hairpin loop to acquire a more stable extended duplex structure. Both bulged adenines form a striking 'base grip' that could be a recognition signal, either in cis for another viral RNA sequence, or in trans for a protein, possibly the NCp. Magnesium binding might be important to promote and stabilize the observed extrahelical conformation of these bulges.

Selected figure(s)

Figure 6.
Figure 6. Stereoviews showing the closing of the deep groove in the vicinity of the bulges and three magnesium cations with direct coordination to phosphates and N7 atoms (trigonal form). (a) Axial coordination of Mg d by the phosphates of G9a and G9b. Mg g and g' are each localized in a pocket formed by the phosphate of A8 and the N7 of G9 of strands b and a, respectively. The ribose of A8a adopts the C3' endo/O4' endo conformation and its base is in the syn conformation, whereas the ribose of A8b is shown here in one of the two conformations (C2' endo). The line of sight is along the noncrystallographic dyad axis. (b) Representative (2F[obs]-F[calc]) electron-density map (light blue), superimposed with the (FMn[obs]-FMg[calc]) Fourier difference map (orange), contoured at 4s around site d and at 6s around sites g and g' (see the Materials and methods section).

The above figure is reprinted by permission from Cell Press: Structure (1999, 7, 1439-1449) copyright 1999.

Figure was selected by an automated process.