1N4L

A DNA analogue of the polypurine tract of HIV-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.240 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Staying Straight with A-tracts: A DNA Analog of the HIV-1 Polypurine Tract

Cote, M.L.Pflomm, M.Georgiadis, M.M.

(2003) J.Mol.Biol. 330: 57-74


  • PubMed Abstract: 
  • The polypurine tract (PPT) from the HIV-1 genome is resistant to digestion by reverse transcriptase following (-)-strand synthesis and is used to prime (+)-strand synthesis during retroviral replication. We have determined the crystal structure of th ...

    The polypurine tract (PPT) from the HIV-1 genome is resistant to digestion by reverse transcriptase following (-)-strand synthesis and is used to prime (+)-strand synthesis during retroviral replication. We have determined the crystal structure of the asymmetric DNA/DNA analog16-mer duplex (CTTTTTAAAAGAAAAG/CTTTTCTTTTAAAAAG) comprising most of the "visible" portion of the RNA:DNA hybrid from the polypurine tract of HIV-1, which was previously reported in a complex with HIV-1 reverse transcriptase. Our 16-mer completely encompasses a 10-mer DNA duplex analog of the HIV-1 PPT. We report here a detailed analysis of our B' form 16-mer DNA structure, including three full pure A-tracts, as well as a comparative structural analysis with polypurine tract and other A-tract-containing nucleic acid structures. Our analysis reveals that the polypurine tract structures share structural features despite being different nucleic acid forms (i.e. DNA:DNA versus RNA:DNA). In addition, the previously reported A-tract-containing DNA molecules bound to topoisomerase I are remarkably similar to our polypurine tract 16-mer structure. On the basis of our analysis, we suggest that the specific topology of long pure A-tracts is remarkably comparable across a wide array of biological environments.


    Related Citations: 
    • Structure of a pseudo-16-mer DNA with stacked guanines and two G-A mispairs coomplexed with the N-terminal fragment of Moloney murine leukemia virus reverse transcriptase
      Cote, M.,Georgaidis, M.M.
      (2001) Acta Crystallogr.,Sect.D 57: 1238
    • Crystal Structures of an N-terminal Fragment from Moloney Murine Leukemia Virus Reverse Transcriptase Complexed with Nucleic Acid: Functional Implications for Template-primer Binding to the Fingers Domain
      Najmudin, S.,Cote, M.L.,Sun, D.,Yohannan, S.,Montano, S.P.,Gu, J.,Georgiadis, M.M.
      (2000) J.Mol.Biol. 296: 613
    • Use of an N-terminal fragment from Moloney murine leukemia virus reverse transcriptase to facilitate crystallization and analysis of a pseudo-16-mer DNA molecule containing G-A mispairs
      Cote, M.L.,Yohannan, S.J.,Georgiadis, M.M.
      (2000) Acta Crystallogr.,Sect.D 56: 1120


    Organizational Affiliation

    Waksman Institute, Rutgers University, Piscataway, NJ 08854-8020, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Reverse Transcriptase
A
255Moloney murine leukemia virusGene Names: gag-pol
EC: 3.1.26.4, 3.1.-.-, 2.7.7.49, 2.7.7.7, 2.7.7.-, 3.4.23.-
Find proteins for P03355 (Moloney murine leukemia virus)
Go to UniProtKB:  P03355
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*CP*TP*TP*TP*TP*TP*AP*AP*AP*AP*GP*AP*AP*AP*AP*G)-3'B16N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*CP*TP*TP*TP*TP*CP*TP*TP*TP*TP*AP*AP*AP*AP*AP*G)-3'D16N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.240 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 54.410α = 90.00
b = 146.222β = 90.00
c = 46.778γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-06-24
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-01-11
    Type: Other
  • Version 1.4: 2017-02-01
    Type: Structure summary