1D1U

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 1120-1131


  • PubMed Abstract: 
  • Complexation with the N-terminal fragment of Moloney murine leukemia virus reverse transcriptase offers a novel method of obtaining crystal structures of nucleic acid duplexes, which can be phased by molecular replacement. This method is somewhat sim ...

    Complexation with the N-terminal fragment of Moloney murine leukemia virus reverse transcriptase offers a novel method of obtaining crystal structures of nucleic acid duplexes, which can be phased by molecular replacement. This method is somewhat similar to the method of using a monoclonal antibody Fab fragment complexed to the molecule of interest in order to obtain crystals suitable for X-ray crystallographic analysis. Here a novel DNA structure including two G-A mispairs in a pseudo-hexadecamer determined at 2.3 A resolution in a complex with the N-terminal fragment is reported. This structure has an asymmetric unit consisting of the protein molecule bound to the blunt end of a DNA 6/10-mer, which is composed of a six-base strand (5'-CTCGTG-3') and a ten-base strand (3'-GAGCACGGCA-5'). The 6/10-mer is thus composed of a six-base-pair duplex with a four-base single-stranded overhang. In the crystal structure, the bases of the overhang are reciprocally paired (symmetry element -x - 1, -y, z), yielding a doubly nicked pseudo-hexadecamer primarily B-form DNA molecule, which has some interesting A-like structural features. The pairing between the single strands results in two standard (G-C) Watson-Crick pairs and two G-A mispairs. The structural DNA model can accommodate either a standard syn or a standard anti conformation for the 5'-terminal adenine of the ten-base strand of the DNA based on analysis of simulated-annealing omit maps. Although the DNA model here includes nicks in the phosphodiester backbone, modeling of an intact phosphodiester backbone results in a very similar DNA model and indicates that the structure is biologically relevant.


    Related Citations: 
    • Crystal Structures of the 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


    Organizational Affiliation

    Waksman Institute and Department of Chemistry, Rutgers University, 190 Frelinghuysen Road, Piscataway, NJ 08854, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (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
DNA (5'-D(*CP*TP*CP*GP*TP*G)-3')B6N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*CP*GP*GP*CP*AP*CP*GP*AP*G)-3')C10N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.230 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 54.738α = 90.00
b = 145.491β = 90.00
c = 46.737γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-04-02
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance