PDBsum entry: 1a1t

Viral protein/RNA

PDB id: 1a1t

Contents

Protein chain

55 a.a. *

DNA/RNA

Metals

_ZN ×2

* Residue conservation analysis

PDB id:

1a1t

Name:

Viral protein/RNA

Title:

Structure of the HIV-1 nucleocapsid protein bound to the sl3 psi-RNA recognition element, nmr, 25 structures

Structure:

Sl3 stem-loop RNA. Chain: b. Engineered: yes. Nucleocapsid protein. Chain: a. Engineered: yes

Source:

Synthetic: yes. Human immunodeficiency virus 1. Organism_taxid: 11676. Strain: nl4-3. Cell_line: bl21. Gene: nc. Expressed in: escherichia coli. Expression_system_taxid: 562.

NMR struc:

25 models

Authors:

R.N.De Guzman,Z.R.Wu,C.C.Stalling,L.Pappalardo,P.N.Borer, M.F.Summers

Key ref:

R.N.De Guzman et al. (1998). Structure of the HIV-1 nucleocapsid protein bound to the SL3 psi-RNA recognition element. Science, 279, 384-388. PubMed id: 9430589 DOI: 10.1126/science.279.5349.384

Date:

15-Dec-97 Release date: 17-Jun-98

Protein chain

Q75677  (Q75677_9HIV1) -  Gag polyprotein (Fragment)

Seq: 107 a.a.

Struc: 55 a.a.*

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

 Gene Ontology (GO) functional annotation 

• Biochemical function: nucleic acid binding (2 terms)

DOI no: 10.1126/science.279.5349.384

Science 279:384-388 (1998)

PubMed id: 9430589

Structure of the HIV-1 nucleocapsid protein bound to the SL3 psi-RNA recognition element.

R.N.De Guzman, Z.R.Wu, C.C.Stalling, L.Pappalardo, P.N.Borer, M.F.Summers.

ABSTRACT

The three-dimensional structure of the human immunodeficiency virus-type 1 (HIV-1) nucleocapsid protein (NC) bound to the SL3 stem-loop recognition element of the genomic Psi RNA packaging signal has been determined by heteronuclear magnetic resonance spectroscopy. Tight binding (dissociation constant, approximately 100 nM) is mediated by specific interactions between the amino- and carboxyl-terminal CCHC-type zinc knuckles of the NC protein and the G7 and G9 nucleotide bases, respectively, of the G6-G7-A8-G9 RNA tetraloop. A8 packs against the amino-terminal knuckle and forms a hydrogen bond with conserved Arg32, and residues Lys3 to Arg10 of NC form a 310 helix that binds to the major groove of the RNA stem and also packs against the amino-terminal zinc knuckle. The structure provides insights into the mechanism of viral genome recognition, explains extensive amino acid conservation within NC, and serves as a basis for the development of inhibitors designed to interfere with genome encapsidation.

Selected figure(s)

Figure 1.
Fig. 1. (A) Amino acid sequence of the HIV-1[NL4-3] NC protein showing the zinc-binding modes of the two CCHC-type zinc knuckles. Residues that contact the RNA in the NC-SL3 complex are denoted^ by open letters; asterisks denote residues involved in intermolecular hydrogen bonding. Abbreviations for the amino acid residues are^ as follows: A, Ala; C, Cys; D, Asp; E, Glu; F, Phe; G, Gly; H, His; I, Ile; K, Lys; M, Met; N, Asn; P, Pro; Q, Gln; R, Arg; T, Thr; V, Val; and W, Trp. (B) Nucleotide sequence and secondary structure of the HIV-1[NL4-3] -sequence (12). The dimer initiation and major splice donor sites are labeled DIS and SD, respectively, and the gag initiation codon (AUG) is given in open letters. (C) Sequence of the RNA construct used in our studies (15).

Figure 4.
Fig. 4. (A) Ribbon diagram of the HIV-1 NC-SL3 -RNA complex. Color code: 3[10] helix, purple; F1 knuckle, blue; linker segment, yellow; F2 knuckle, green; zinc atoms, white spheres; RNA, gray, except for the G6 (light green), G7 (pink), A^8 (violet), and G9 (orange) nucleobases. (B) Space-filling image of the NC^ protein [rotated ~90° relative to (A)] showing the G9-F1, A^8-F1, and G7-F2 interactions, the orientation of the 3[10] helix in the RNA^ major groove, and the extensive intra-NC interactions that occur upon RNA binding [colors as in (A)]. (C) GRASP image showing the nature of G9 nucleobase binding to the hydrophobic cleft of the F1 knuckle^ (intermolecular hydrogen bonds are shown in green). G7 binds the F2 knuckle in a similar manner. (D) Space-filling representation of the SL3 RNA in the NC-SL3 complex [same orientation as in (A)] showing relative proximities of conserved NC basic^ residues (blue) to the RNA phosphodiesters (red). Conserved residue^ Asn5, which forms hydrogen bonds with C^11-NH[2], G10-N7, and G9-O2 , is shown in purple, and the hydrogen bond between conserved^ Arg32 and A^8 is also shown.

The above figures are reprinted by permission from the AAAs: Science (1998, 279, 384-388) copyright 1998.

Figures were selected by an automated process.