PDBsum entry: 1u6p

Viral protein/RNA

PDB id: 1u6p

Contents

Protein chain

56 a.a. *

DNA/RNA

Metals

_ZN

* Residue conservation analysis

PDB id:

1u6p

Name:

Viral protein/RNA

Title:

Nmr structure of the mlv encapsidation signal bound to the nucleocapsid protein

Structure:

Gag polyprotein. Chain: a. Fragment: nucleoprotein p10. Synonym: mmlv nucleocapsid protein. Engineered: yes. 101-mer. Chain: b. Engineered: yes. Other_details: mlv encapsidation signal RNA

Source:

Moloney murine leukemia virus. Organism_taxid: 11801. Gene: gag. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: this sequence was synthesized by in vitro transcription using a linearized DNA plasmid as template

NMR struc:

20 models

Authors:

V.D'Souza,M.F.Summers

Key ref:

V.D'Souza and M.F.Summers (2004). Structural basis for packaging the dimeric genome of Moloney murine leukaemia virus. Nature, 431, 586-590. PubMed id: 15457265 DOI: 10.1038/nature02944

Date:

30-Jul-04 Release date: 02-Nov-04

Protein chain

P03332  (GAG_MLVMS) -  Gag polyprotein

Seq: 538 a.a.

Struc: 56 a.a.

 Gene Ontology (GO) functional annotation 

• Biochemical function: nucleic acid binding (2 terms)

DOI no: 10.1038/nature02944

Nature 431:586-590 (2004)

PubMed id: 15457265

Structural basis for packaging the dimeric genome of Moloney murine leukaemia virus.

V.D'Souza, M.F.Summers.

ABSTRACT

All retroviruses specifically package two copies of their genomes during virus assembly, a requirement for strand-transfer-mediated recombination during reverse transcription. Genomic RNA exists in virions as dimers, and the overlap of RNA elements that promote dimerization and encapsidation suggests that these processes may be coupled. Both processes are mediated by the nucleocapsid domain (NC) of the retroviral Gag polyprotein. Here we show that dimerization-induced register shifts in base pairing within the Psi-RNA packaging signal of Moloney murine leukaemia virus (MoMuLV) expose conserved UCUG elements that bind NC with high affinity (dissociation constant = 75 +/- 12 nM). These elements are base-paired and do not bind NC in the monomeric RNA. The structure of the NC complex with a 101-nucleotide 'core encapsidation' segment of the MoMuLV Psi site reveals a network of interactions that promote sequence- and structure-specific binding by NC's single CCHC zinc knuckle. Our findings support a structural RNA switch mechanism for genome encapsidation, in which protein binding sites are sequestered by base pairing in the monomeric RNA and become exposed upon dimerization to promote packaging of a diploid genome.

Selected figure(s)

Figure 2.
Figure 2: Comparison of the guanosine binding sites of the MoMuLV and HIV-1 zinc knuckles. a, MoMuLV zinc knuckle in NC -m CES. b, HIV-1 zinc knuckle in NC -SL3 (ref. 16). For comparison, the numbering scheme used for both zinc knuckles begins with the first cysteine labelled Cys 1 (this figure only). The zinc atom (cyan) and cysteine (yellow) and histidine (blue) side chains are shown.

Figure 4.
Figure 4: Structural changes in the Psi--site that seem to serve as a switch for the selective binding of NC to the dimer. Conserved UCUG bases (red) are base paired in the monomeric state and become exposed for NC binding upon dimerization. Dimerization may promote exposure of additional downstream UCUG elements to enhance the specific packaging of a diploid genome.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2004, 431, 586-590) copyright 2004.

Figures were selected by the author.