HIV Databases HIV Databases home HIV Databases home
HIV sequence database



HIV-1 RNA Structures Index


Tutorials and Museum Exhibits

(Please CHECK to make sure you have installed the CHIME plug-in into your browser and that it is functioning, before proceeding. A troubleshooting guide is available.)

A tutorial on HIV-1 dimer initiation complex "kissing loop" structure 1BAU by students Ann Palcisco and Lauren Stancik at Kenyon College.
This tutorial does not work in Internet Explorer. It only works in Netscape Communicator 4.7.


PDB Structure Entries

Use the buttons below each entry in the list to get the PubMed entry, protein structure database (PDB) entry, open a Protein Explorer session with the entry, or get the NCBI entry (allowing Cn3D viewing) of the entry.
1A1T: Science 1998 Jan 16;279(5349):384-8.
Gag p7 nucleocapsid (amino acids 1-55 in p7; 378-432 in Gag precursor of HXB2) bound to Psi element (RNA packaging signal between LTR and gag gene) bases 763-782 in HXB2: 25 NMR structures.

1F6U: J Mol Biol. 2000 Aug 11;301(2):491-511.
NMR Structure Of The HIV-1 Nucleocapsid Protein Bound To Stem-Loop SL2 Of The Psi-element RNA packaging signal.

1LVJ: Chem Biol 2002 Jun;9(6):707-12.
NMR structure of Tar RNA complexed with a Tat-Tar interaction nanomolar inhibitor that was identified by computational screening.

1ANR: Nucleic Acids Res 1996 Oct 15;24(20):3974-81.
HIV-1 Tar element in Argininamide Complex, NMR, 20 Structures.

1ARJ: J Mol Biol 1995 Oct 20;253(2):313-32.
HIV-1 Tar element in Argininamide Complex, NMR, 20 Structures.

1QD3: J Biol Chem. 2000 Jul 7;275(27):20660-6. Biochemistry. 1998 Apr 21;37(16):5549-57.
HIV-1 Tar RNA/Neomycin B Complex.

1AJU: J Mol Biol 1997 Apr 4;267(3):624-39.
HIV-2 Tar element in argininamide complex, NMR, 20 structures.

1AKX: J Mol Biol 1997 Apr 4;267(3):624-39.
HIV-2 Tar element in argininamide complex, NMR, minimized structure.

1BAU: Nat Struct Biol 1998 Jun;5(6):432-6.
NMR structure of the dimer initiation complex of HIV-1 genomic RNA, minimized average structure.

1BIV: Chem Biol 1995 Dec;2(12):827-40.
Bovine Immunodeficiency Virus Tat-Tar complex, NMR, 5 structures.

1GTC: Biochemistry 1996 Aug 27;35(34):11070-80.
HIV-1 Okazaki fragment, DNA-RNA chimera, NMR, 11 structures.

1PJY: Nucleic Acids Res. 31 pp. 4326 (2003).
NMR Solution Structure of the HIV-1 Gag-Pol Frameshift-Inducing Stem-Loop RNA.

No PDB entry yet: J Mol Biol. 331(3):571-583 (2003).
The frameshift stimulatory signal of human immunodeficiency virus type 1 group O is a pseudoknot.
Structure available from authors on request.

1I9F: Chem Biol 2001 May;8(5):511-20.
HIV-1 Rev-Responsive Element in env gene region, in complex with a peptide.

1ETF: Science 1996 Sep 13;273(5281):1547-51.
HIV-1 Rev-Responsive Element in env gene region, in complex with Rev protein.

1ETG: Science 1996 Sep 13;273(5281):1547-51.
HIV-1 Rev-Responsive Element in env gene region, in complex with Rev protein.

1EBR: Science 1996 Sep 13;273(5281):1547-51.
HIV-1 Rev-Responsive Element in env gene region, in complex with Rev protein.

1EBS: Science 1996 Sep 13;273(5281):1547-51.
HIV-1 Rev-Responsive Element in env gene region, in complex with Rev protein.

1EBQ: J Mol Biol 1996 Dec 20;264(5):863-77.
HIV-1 Rev-Responsive Element in env gene region, in complex with Rev protein.

1RPV: Biochemistry 1995 Jul 4;34(26):8242-9.
HIV-1 Rev-Responsive Element in env gene region, in complex with Rev protein.

1G70: Nat Struct Biol. 2001 Feb;8(2):146-50.
HIV-1 Rev-Responsive Element in env gene region, in complex with Rev protein.

1ULL: Nat Struct Biol 1996 Dec;3(12):1026-33.
HIV-1 Rev-Responsive Element in env gene region, in complex with Rev protein, 7 NMR structures.

484D: Chem Biol 1999 Sep;6(9):657-69.
HIV-1 Rev-Responsive Element in env gene region, in complex with Rev protein, 22 NMR structures.

Publications on RNA Structures

HIV-1 TAR Element
Richter S, Cao H, Rana TM.
Specific HIV-1 TAR RNA loop sequence and functional groups are required for human cyclin T1-Tat-TAR ternary complex formation.
Biochemistry. 2002 May 21;41(20):6391-7.
PMID: 12009901

Interferon Responsive Element in LTR
Battistini A, Marsili G, Sgarbanti M, Ensoli B, Hiscott J.
IRF regulation of HIV-1 long terminal repeat activity.
J Interferon Cytokine Res. 2002 Jan;22(1):27-37. Review.
PMID: 11846973

HIV-1 RNA genomic RNA packaging signal (Psi Elements) between LTR and gag gene.
Harrison GP, Miele G, Hunter E, Lever AM.
Functional analysis of the core human immunodeficiency virus type 1 packaging signal in a permissive cell line.
J Virol. 1998 Jul;72(7):5886-96.
PMID: 9621050

HIV-1 RNA genomic RNA packaging signal (Psi Elements) between LTR and gag gene.
Lawrence DC, Stover CC, Noznitsky J, Wu Z, Summers MF.
Structure of the intact stem and bulge of HIV-1 Psi-RNA stem-loop SL1.
J Mol Biol. 2003 Feb 14;326(2):529-42.
PMID: 12559920

HIV-1 RNA genomic RNA packaging signal (Psi Elements) between LTR and gag gene.
Clever J, Sassetti C, Parslow TG.
RNA secondary structure and binding sites for gag gene products in the 5' packaging signal of human immunodeficiency virus type 1.
J Virol. 1995 Apr;69(4):2101-9.
PMID: 7884856

HIV-1 Gag protein zinc knuckles bind to Psi Element packaging signal
Amarasinghe GK, De Guzman RN, Turner RB, Chancellor KJ, Wu ZR, Summers MF.
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. 2000 Aug 11;301(2):491-511.
PMID: 10926523

Env C1 region
Peleg O, Brunak S, Trifonov EN, Nevo E, Bolshoy A.
RNA secondary structure and sequence conservation in C1 region of human immunodeficiency virus type 1 env gene.
AIDS Res Hum Retroviruses. 2002 Aug 10;18(12):867-78.
PMID: 12201910

HIV-1 Rev-Responsive (RRE) Element
L.W. Hung, E.L. Holbrook, and S.R. Holbrook .
Key Domain in HIV-1 Gene Shows Unexpected Flexibility
Advanced Light Source.

HIV-1 Rev-Responsive (RRE) Element
Hung LW, Holbrook EL, Holbrook SR.
The crystal structure of the Rev binding element of HIV-1 reveals novel base pairing and conformational variability.
Proc Natl Acad Sci U S A. 2000 May 9;97(10):5107-12.
PMID: 10792052

HIV-1 Gag-Pol -1 Translational Frameshifting Stem-Loop
Baril M, Dulude D, Gendron K, Lemay G, Brakier-Gingras L.
Efficiency of a programmed -1 ribosomal frameshift in the different subtypes of the human immunodeficiency virus type 1 group M.
RNA. 2003 Oct;9(10):1246-53.
PMID: 13130138


last modified: Thu Jan 14 15:02 2010


Questions or comments? Contact us at seq-info@lanl.gov.

 
Operated by Los Alamos National Security, LLC, for the U.S. Department of Energy's National Nuclear Security Administration
Copyright © 2005-2012 LANS LLC All rights reserved | Disclaimer/Privacy

Dept of Health & Human Services Los Alamos National Institutes of Health