1PJO

Crystal Structure of an RNA/DNA hybrid of HIV-1 PPT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.156 
  • R-Value Work: 0.117 

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This is version 1.2 of the entry. See complete history


Literature

An Unusual Sugar Conformation in the Structure of an RNA/DNA Decamer of the Polypurine Tract May Affect Recognition by RNase H

Kopka, M.L.Lavelle, L.Han, G.W.Ng, H.-L.Dickerson, R.E.

(2003) J Mol Biol 334: 653-665

  • DOI: 10.1016/j.jmb.2003.09.057
  • Primary Citation of Related Structures:  
    1PJG, 1PJO

  • PubMed Abstract: 
  • Retroviral conversion of single-stranded RNA into double-stranded DNA requires priming for each strand. While host cellular t-RNA serves as primer for the first strand, the viral polypurine tract (PPT) is primer for the second. Therefore, polypurine tracts of retroviruses are essential for viral replication by reverse transcriptase (RT) ...

    Retroviral conversion of single-stranded RNA into double-stranded DNA requires priming for each strand. While host cellular t-RNA serves as primer for the first strand, the viral polypurine tract (PPT) is primer for the second. Therefore, polypurine tracts of retroviruses are essential for viral replication by reverse transcriptase (RT). These purine tracts are resistant to cleavage during first strand synthesis. In obtaining the primer for second strand synthesis, the RNase H function of RT must cleave the PPT exactly for in vivo transcription to proceed efficiently and proper integration to occur. At the RNase H active site the protein makes contacts primarily along the backbone, with hydrogen bonds to the sugar-phosphate oxygen atoms. A high-resolution structure (1.10A) of the first ten base-pairs of the RNA/DNA hybrid PPT, r-(c-a-a-a-g-a-a-a-a-g)/d-(C-T-T-T-T-C-T-T-T-G), contains the highly deformable r-(a-g-a) steps found in retroviral polypurine tracts. This r-(a-g-a) motif is utilized in the "unzipping" or unpairing of bases that occurs when RT binds a malleable PPT. Another unusual feature found in our high-resolution PPT structure is the sugar switch at RNA adenine 2. All the RNA sugars are the expected C3'-endo, except sugar 2, which is C2'-endo, characteristic of B-form sugars. This local A-to-B conversion adversely affects the pattern of hydrogen bonds from protein to sugar-phosphate backbone, disrupting the catalytic site. Disruption could cause the enzyme to pause at the 5'-end of the PPT, leaving it intact. Pyrimidine-purine (YR) steps are most deformable and the T-A step especially can undergo A-to-B transitions readily.


    Related Citations: 
    • Direct Methods Determination of an RNA/DNA Hybrid Decamer at 1.15A Resolution
      Han, G.W.
      (2001) Acta Crystallogr D Biol Crystallogr 57: 213
    • Crystal Structure of an RNA/DNA Hybrid Reveals Novel Intermolecular Intercalation: Dimer Formation by Base-pair Swapping
      Han, G.W., Kopka, M.L., Langs, D., Sawaya, M.R., Dickerson, R.E.
      (2003) To be published --: --

    Organizational Affiliation

    Molecular Biology Institute, University of California, Los Angeles, CA 90095-1570, USA. kopka@mbi.ucla.edu



Macromolecules

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Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-R(*CP*AP*AP*AP*GP*AP*AP*AP*AP*G)-3'A 10N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-D(*CP*TP*TP*TP*TP*CP*TP*TP*TP*G)-3'B 10N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.156 
  • R-Value Work: 0.117 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 25.595α = 90
b = 40.755β = 90
c = 45.74γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
SHELXL-97refinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-12-09
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance