2N4Y | pdb_00002n4y

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

• PDB DOI: https://doi.org/10.2210/pdb2N4Y/pdb
• BMRB: 25686
• NAKB: 2N4Y

• Classification: DNA
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2015-07-02 Released: 2016-06-29 
• Deposition Author(s): DeNicola, B., Lech, C.J., Heddi, B., Regmi, S., Frasson, I., Perrone, R., Richter, S.N., Phan, A.T.

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Experimental Data Snapshot

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

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

• PubMed: 27298260 
• DOI: https://doi.org/10.1093/nar/gkw432
• Primary Citation Related Structures: 
  2N4Y


• 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 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.

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Organizational Affiliation: 
• School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore Department of Molecular Medicine, University of Padua, Italy.
School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore.
Department of Molecular Medicine, University of Padua, Italy.
Department of Molecular Medicine, University of Padua, Italy [e-mail].
School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore [e-mail].

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 6.95 kDa 
• Atom Count: 462 
• Modeled Residue Count: 22 
• Deposited Residue Count: 22 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
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')	A	22	synthetic construct

Experimental Data & Validation

Experimental Data

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-06-29 
Deposition Author(s): DeNicola, B., Lech, C.J., Heddi, B., Regmi, S., Frasson, I., Perrone, R., Richter, S.N., Phan, A.T.

Revision History  

• Version 1.0: 2016-06-29
  Type: Initial release
  
• Version 1.1: 2017-06-07
  Changes: Database references
• Version 1.2: 2023-06-14
  Changes: Data collection, Database references, Other
• Version 1.3: 2024-05-15
  Changes: Data collection, Database references