2N4Y

Structure and possible function of a G-quadruplex in the long terminal repeat of the proviral HIV-1 genome


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure and possible function of a G-quadruplex in the long terminal repeat of the proviral HIV-1 genome.

De Nicola, B.Lech, C.J.Heddi, B.Regmi, S.Frasson, I.Perrone, R.Richter, S.N.Phan, A.T.

(2016) Nucleic Acids Res 44: 6442-6451

  • DOI: 10.1093/nar/gkw432
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The long terminal repeat (LTR) of the proviral human immunodeficiency virus (HIV)-1 genome is integral to virus transcription and host cell infection. The guanine-rich U3 region within the LTR promoter, previously shown to form G-quadruplex structure ...

    The long terminal repeat (LTR) of the proviral human immunodeficiency virus (HIV)-1 genome is integral to virus transcription and host cell infection. The guanine-rich U3 region within the LTR promoter, previously shown to form G-quadruplex structures, represents an attractive target to inhibit HIV transcription and replication. In this work, we report the structure of a biologically relevant G-quadruplex within the LTR promoter region of HIV-1. The guanine-rich sequence designated LTR-IV forms a well-defined structure in physiological cationic solution. The nuclear magnetic resonance (NMR) structure of this sequence reveals a parallel-stranded G-quadruplex containing a single-nucleotide thymine bulge, which participates in a conserved stacking interaction with a neighboring single-nucleotide adenine loop. Transcription analysis in a HIV-1 replication competent cell indicates that the LTR-IV region may act as a modulator of G-quadruplex formation in the LTR promoter. Consequently, the LTR-IV G-quadruplex structure presented within this work could represent a valuable target for the design of HIV therapeutics.


    Organizational Affiliation

    School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore phantuan@ntu.edu.sg.



Macromolecules

Find similar nucleic acids by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA_(5'-D(*CP*TP*GP*GP*GP*CP*GP*GP*GP*AP*CP*TP*GP*GP*GP*GP*AP*GP*TP*GP*GP*T)-3')A22synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 
  • OLDERADO: 2N4Y Olderado

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-06-29
    Type: Initial release
  • Version 1.1: 2017-06-07
    Changes: Database references