3PA0

Crystal Structure of Chiral Gamma-PNA with Complementary DNA Strand: Insight Into the Stability and Specificity of Recognition an Conformational Preorganization


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Crystal structure of chiral gammaPNA with complementary DNA strand: insights into the stability and specificity of recognition and conformational preorganization.

Yeh, J.I.Shivachev, B.Rapireddy, S.Crawford, M.J.Gil, R.R.Du, S.Madrid, M.Ly, D.H.

(2010) J Am Chem Soc 132: 10717-10727

  • DOI: https://doi.org/10.1021/ja907225d
  • Primary Citation of Related Structures:  
    3PA0

  • PubMed Abstract: 

    We have determined the structure of a PNA-DNA duplex to 1.7 A resolution by multiple-wavelength anomalous diffraction phasing method on a zinc derivative. This structure represents the first high-resolution 3D view of a hybrid duplex containing a contiguous chiral PNA strand with complete gamma-backbone modification ("gammaPNA"). Unlike the achiral counterpart, which adopts a random-fold, this particular gammaPNA is already preorganized into a right-handed helix as a single strand. The new structure illustrates the unique characteristics of this modified PNA, possessing conformational flexibility while maintaining sufficient structural integrity to ultimately adopt the preferred P-helical conformation upon hybridization with DNA. The unusual structural adaptability found in the gammaPNA strand is crucial for enabling the accommodation of backbone modifications while constraining conformational states. In conjunction with NMR analysis characterizing the structures and substructures of the individual building blocks, these results provide unprecedented insights into how this new class of chiral gammaPNA is preorganized and stabilized, before and after hybridization with a cDNA strand. Such knowledge is crucial for the future design and development of PNA for applications in biology, biotechnology, and medicine.


  • Organizational Affiliation

    Department of Structural Biology, University of Pittsburgh Medical School 1036 BST3, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15260, USA. jiyeh@pitt.edu


Macromolecules

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Entity ID: 1
MoleculeChains LengthOrganismImage
DNA 5'-D(*AP*TP*CP*TP*GP*TP*GP*GP*TP*C)-3'
A, B
10synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
PEPTIDE NUCLEIC ACID
C, D
11synthetic construct
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.19α = 90
b = 52.57β = 90
c = 61.15γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SHELXmodel building
SHELXL-97refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-12-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Database references, Derived calculations