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 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.274 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1093/emboj/20.6.1449
  • Also Cited By: 2I5J, 4PQU, 4PUO, 4PWD, 4Q0B

  • 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 re ...

    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

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
HIV-1 REVERSE TRANSCRIPTASE
A
553Human immunodeficiency virus type 1 group M subtype BGene Names: gag-pol
EC: 3.4.23.16, 3.1.-.-, 2.7.7.49, 2.7.7.7, 3.1.26.13, 2.7.7.-, 3.1.13.2
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P03366
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
HIV-1 REVERSE TRANSCRIPTASE
B
425Human immunodeficiency virus type 1 group M subtype BGene Names: gag-pol
EC: 3.4.23.16, 3.1.-.-, 2.7.7.49, 2.7.7.7, 3.1.26.13, 2.7.7.-, 3.1.13.2
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P03366
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
FAB-28 MONOCLONAL ANTIBODY FRAGMENT LIGHT CHAIN
C
214N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
FAB-28 MONOCLONAL ANTIBODY FRAGMENT HEAVY CHAIN
D
220N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 1
MoleculeChainsLengthOrganism
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'E23N/A
Entity ID: 2
MoleculeChainsLengthOrganism
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'F22N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.274 
  • Space Group: P 32 1 2
Unit Cell:
Length (Å)Angle (°)
a = 166.160α = 90.00
b = 166.160β = 90.00
c = 218.810γ = 120.00
Software Package:
Software NamePurpose
X-PLORrefinement
DENZOdata reduction
X-PLORmodel building
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-03-26
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance