PDBsum entry: 1f6u

Structural protein/RNA

PDB id: 1f6u

Contents

Protein chain

56 a.a. *

DNA/RNA

Metals

_ZN ×2

* Residue conservation analysis

PDB id:

1f6u

Name:

Structural protein/RNA

Title:

Nmr structure of the HIV-1 nucleocapsid protein bound to stem-loop sl2 of the psi-RNA packaging signal. Implications for genome recognition

Structure:

HIV-1 nucleocapsid protein. Chain: a. Engineered: yes. HIV-1 stem-loop sl2 from psi-RNA packaging. Chain: b. Engineered: yes

Source:

Human immunodeficiency virus 1. Organism_taxid: 11676. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes

NMR struc:

20 models

Authors:

G.K.Amarasinghe,R.N.De Guzman,R.B.Turner,K.J.Chancellor, M.F.Summers

Key ref:

G.K.Amarasinghe et al. (2000). NMR structure of the HIV-1 nucleocapsid protein bound to stem-loop SL2 of the psi-RNA packaging signal. Implications for genome recognition. J Mol Biol, 301, 491-511. PubMed id: 10926523 DOI: 10.1006/jmbi.2000.3979

Date:

23-Jun-00 Release date: 09-Oct-00

Protein chain

P35963  (POL_HV1Y2) -  Gag-Pol polyprotein

Seq: 1435 a.a.

Struc: 56 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class 1: E.C.2.7.7.49 - RNA-directed Dna polymerase.
• Reaction: Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
• Enzyme class 2: E.C.2.7.7.7 - DNA-directed Dna polymerase.
• Reaction: Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
• Enzyme class 3: E.C.3.1.13.2 - Exoribonuclease H.
• Reaction: Exonucleolytic cleavage to 5'-phosphomonoester oligonucleotides in both 5'- to 3'- and 3'- to 5'-directions.
• Enzyme class 4: E.C.3.1.26.13 - Retroviral ribonuclease H.
• Enzyme class 5: E.C.3.4.23.16 - HIV-1 retropepsin.
• Reaction: Specific for a P1 residue that is hydrophobic, and P1' variable, but often Pro.

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• Biochemical function: nucleic acid binding (2 terms)

reference

DOI no: 10.1006/jmbi.2000.3979

J Mol Biol 301:491-511 (2000)

PubMed id: 10926523

NMR structure of the HIV-1 nucleocapsid protein bound to stem-loop SL2 of the psi-RNA packaging signal. Implications for genome recognition.

G.K.Amarasinghe, R.N.De Guzman, R.B.Turner, K.J.Chancellor, Z.R.Wu, M.F.Summers.

ABSTRACT

The RNA genome of the human immunodeficiency virus type-1 (HIV-1) contains a approximately 120 nucleotide Psi-packaging signal that is recognized by the nucleocapsid (NC) domain of the Gag polyprotein during virus assembly. The Psi-site contains four stem-loops (SL1-SL4) that possess overlapping and possibly redundant functions. The present studies demonstrate that the 19 residue SL2 stem-loop binds NC with affinity (K(d)=110(+/-50) nM) similar to that observed for NC binding to SL3 (K(d)=170(+/-65) nM) and tighter than expected on the basis of earlier work, suggesting that NC-SL2 interactions probably play a direct role in the specific recognition and packaging of the full-length, unspliced genome. The structure of the NC-SL2 complex was determined by heteronuclear NMR methods using (15)N,(13)C-isotopically labeled NC protein and SL2 RNA. The N and C-terminal "zinc knuckles" (Cys-X(2)-Cys-X(4)-His-X(4)-Cys; X=variable amino acid) of HIV-1 NC bind to exposed guanosine bases G9 and G11, respectively, of the G8-G9-U10-G11 tetraloop, and residues Lys3-Lys11 of the N-terminal tail forms a 3(10) helix that packs against the proximal zinc knuckle and interacts with the RNA stem. These structural features are similar to those observed previously in the NMR structure of NC bound to SL3. Other features of the complex are substantially different. In particular, the N-terminal zinc knuckle interacts with an A-U-A base triple platform in the minor groove of the SL2 RNA stem, but binds to the major groove of SL3. In addition, the relative orientations of the N and C-terminal zinc knuckles differ in the NC-SL2 and NC-SL3 complexes, and the side-chain of Phe6 makes minor groove hydrophobic contacts with G11 in the NC-SL2 complex but does not interact with RNA in the NC-SL3 complex. Finally, the N-terminal helix of NC interacts with the phosphodiester backbone of the SL2 RNA stem mainly via electrostatic interactions, but does not bind in the major groove or make specific H-bonding contacts as observed in the NC-SL3 structure. These findings demonstrate that NC binds in an adaptive manner to SL2 and SL3 via different subsets of inter and intra-molecular interactions, and support a genome recognition/packaging mechanism that involves interactions of two or more NC domains of assembling HIV-1 Gag molecules with multiple Psi-site stem-loop packaging elements during the early stages of retrovirus assembly.

Selected figure(s)

Figure 7.
Figure 7. Two views of a representative NC-SL2 structure that differ by a vert, similar 180° rotation about the z-axis. The nucleobases of residues G9, U10 and G11 are colored green, orange and purple, respectively. The side-chains of selected basic residues are colored blue, and the zinc atoms are displayed as silver spheres. (a) The N-terminal zinc knuckle packs against A15 of the A5-U14-A15 base triple, and the side-chains of Lys34 and Lys47 are poised to form salt-bridges with phosphodiester groups. (b) The side-chains of Lys3 and Arg7 are also poised to interact with phosphodiester groups of SL2.

Figure 9.
Figure 9. Hydrophobic contacts and hydrogen bonding interactions associated with the packing of the nucleobase of G11 into the hydrophobic cleft of the N-terminal zinc knuckle.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 301, 491-511) copyright 2000.

Figures were selected by the author.