1HYS

CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE IN COMPLEX WITH A POLYPURINE TRACT RNA:DNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.274 

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This is version 1.4 of the entry. See complete history. 


Literature

Crystal structure of HIV-1 reverse transcriptase in complex with a polypurine tract RNA:DNA.

Sarafianos, S.G., Das, K., Tantillo, C., Clark Jr., A.D., Ding, J., Whitcomb, J.M., Boyer, P.L., Hughes, S.H., Arnold, E.

(2001) EMBO J 20: 1449-1461

  • DOI: https://doi.org/10.1093/emboj/20.6.1449
  • Primary Citation of Related Structures:  
    1HYS

  • PubMed Abstract: 

    • We have determined the 3.0 A resolution structure of wild-type HIV-1 reverse transcriptase in complex with an RNA:DNA oligonucleotide whose sequence includes a purine-rich segment from the HIV-1 genome called the polypurine tract (PPT). The PPT is resistant to ribonuclease H (RNase H) cleavage and is used as a primer for second DNA strand synthesis ...

    We have determined the 3.0 A resolution structure of wild-type HIV-1 reverse transcriptase in complex with an RNA:DNA oligonucleotide whose sequence includes a purine-rich segment from the HIV-1 genome called the polypurine tract (PPT). The PPT is resistant to ribonuclease H (RNase H) cleavage and is used as a primer for second DNA strand synthesis. The 'RNase H primer grip', consisting of amino acids that interact with the DNA primer strand, may contribute to RNase H catalysis and cleavage specificity. Cleavage specificity is also controlled by the width of the minor groove and the trajectory of the RNA:DNA, both of which are sequence dependent. An unusual 'unzipping' of 7 bp occurs in the adenine stretch of the PPT: an unpaired base on the template strand takes the base pairing out of register and then, following two offset base pairs, an unpaired base on the primer strand re-establishes the normal register. The structural aberration extends to the RNase H active site and may play a role in the resistance of PPT to RNase H cleavage.

    Organizational Affiliation: 

    Center for Advanced Biotechnology and Medicine and Rutgers University Chemistry Department, 679 Hoes Lane, Piscataway, NJ 08854-5638, USA.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
HIV-1 REVERSE TRANSCRIPTASEC [auth A]553Human immunodeficiency virus 1Mutation(s): 1 
Gene Names: POL
EC: 2.7.7.49 (PDB Primary Data), 3.4.23.16 (UniProt), 2.7.7.7 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
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Go to UniProtKB:  P03366
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UniProt GroupP03366
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
HIV-1 REVERSE TRANSCRIPTASED [auth B]425Human immunodeficiency virus 1Mutation(s): 1 
Gene Names: POL
EC: 2.7.7.49 (PDB Primary Data), 3.4.23.16 (UniProt), 2.7.7.7 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
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Go to UniProtKB:  P03366
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UniProt GroupP03366
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
FAB-28 MONOCLONAL ANTIBODY FRAGMENT LIGHT CHAINE [auth C]214Mus musculusMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
FAB-28 MONOCLONAL ANTIBODY FRAGMENT HEAVY CHAINF [auth D]220Mus musculusMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-R(*UP*CP*AP*GP*CP*CP*AP*CP*UP*UP*UP*UP*UP*AP*AP*AP*AP*GP*AP*AP*AP*AP*G)-3'A [auth E]23N/A
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Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-D(*CP*TP*TP*TP*TP*CP*TP*TP*TP*TP*AP*AP*AP*AP*AP*GP*TP*GP*GP*CP*TP*G)-3'B [auth F]22N/A
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.274 
  • Space Group: P 32 1 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 166.16α = 90
b = 166.16β = 90
c = 218.81γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-03-26
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-10-27
    Changes: Database references
  • Version 1.4: 2023-08-09
    Changes: Data collection, Refinement description