Biological Assembly 1  

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 33785.55 
• Atom Count: 2366 
• Residue Count: 271 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

1ZTW

d(CTTAATTCGAATTAAG) complexed with Moloney Murine Leukemia Virus Reverse Transcriptase catalytic fragment

• DOI: 10.2210/pdb1ZTW/pdb
• NDB: PD0679

• Classification: TRANSFERASE/DNA
• Organism(s): Moloney murine leukemia virus (isolate Shinnick)
• Expression System: Escherichia coli


• Deposited: 2005-05-27 Released: 2005-08-30 
• Deposition Author(s): Goodwin, K.D., Long, E.C., Georgiadis, M.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.264 
• R-Value Work: 0.227 

Literature

A host-guest approach for determining drug-DNA interactions: an example using netropsin.

Goodwin, K.D., Long, E.C., Georgiadis, M.M.

(2005) Nucleic Acids Res. 33: 4106-4116

• PubMed: 16049022 
• DOI: 10.1093/nar/gki717
• Primary Citation of Related Structures:  
  1ZTT


• PubMed Abstract: 
  

Netropsin is a well-characterized DNA minor groove binding compound that serves as a model for the study of drug-DNA interactions. Our laboratory has developed a novel host-guest approach to study drug-DNA interactions in which the host, the N-terminal fragment of Moloney murine leukemia virus reverse transcriptase (MMLV RT) is co-crystallized with a DNA oligonucleotide guest in the presence and absence of drug. We have co-crystallized netropsin with the RT fragment bound to the symmetric 16mer d(CTTAATTCGAATTAAG)2 and determined the structure of the complex at 1.85 A. In contrast to previously reported netropsin-DNA structures, our oligonucleotide contains two AATT sites that bind netropsin with flanking 5' and 3' sequences that are not symmetric. The asymmetric unit of the RT fragment-DNA-netropsin crystals contains one protein molecule and one-half of the 16mer with one netropsin molecule bound. The guanidinium moiety of netropsin binds in a narrow part of the minor groove, while the amidinium is bound in the widest region within the site. We compare this structure to other Class I netropsin-DNA structures and find that the asymmetry of minor groove widths in the AATT site contributes to the orientation of netropsin within the groove while hydrogen bonding patterns vary in the different structures.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, IN 46202, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Reverse transcriptase	A	255	Moloney murine leukemia virus (isolate Shinnick)	Mutation(s): 0  Gene Names: gag-pol
Find proteins for P03355 (Moloney murine leukemia virus (isolate Shinnick)) Go to UniProtKB:  P03355

Entity ID: 1
Molecule	Chains	Length	Organism
CTTAATTC	B	8	N/A

Entity ID: 2
Molecule	Chains	Length	Organism
GAATTAAG	G	8	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.264 
• R-Value Work: 0.227 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 54.934	α = 90.00
b = 145.746	β = 90.00
c = 46.855	γ = 90.00

Software Package:

Software Name	Purpose
CNS	refinement
SCALEPACK	data scaling
AMoRE	phasing
HKL-2000	data reduction
HKL-2000	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-05-27 
• Released Date: 2005-08-30 
• Deposition Author(s): Goodwin, K.D., Long, E.C., Georgiadis, M.M.

Revision History 

• Version 1.0: 2005-08-30
  Type: Initial release
• Version 1.1: 2008-04-30
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance