4XPC

Crystal structure of 5'- CTTATAAATTTATAAG in a host-guest complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis for a six nucleotide genetic alphabet.

Georgiadis, M.M.Singh, I.Kellett, W.F.Hoshika, S.Benner, S.A.Richards, N.G.

(2015) J Am Chem Soc 137: 6947-6955

  • DOI: 10.1021/jacs.5b03482
  • Primary Citation of Related Structures:  
    4XNO, 4XO0, 4XPE, 4XPC

  • PubMed Abstract: 
  • Expanded genetic systems are most likely to work with natural enzymes if the added nucleotides pair with geometries that are similar to those displayed by standard duplex DNA. Here, we present crystal structures of 16-mer duplexes showing this to be ...

    Expanded genetic systems are most likely to work with natural enzymes if the added nucleotides pair with geometries that are similar to those displayed by standard duplex DNA. Here, we present crystal structures of 16-mer duplexes showing this to be the case with two nonstandard nucleobases (Z, 6-amino-5-nitro-2(1H)-pyridone and P, 2-amino-imidazo[1,2-a]-1,3,5-triazin-4(8H)one) that were designed to form a Z:P pair with a standard "edge on" Watson-Crick geometry, but joined by rearranged hydrogen bond donor and acceptor groups. One duplex, with four Z:P pairs, was crystallized with a reverse transcriptase host and adopts primarily a B-form. Another contained six consecutive Z:P pairs; it crystallized without a host in an A-form. In both structures, Z:P pairs fit canonical nucleobase hydrogen-bonding parameters and known DNA helical forms. Unique features include stacking of the nitro group on Z with the adjacent nucleobase ring in the A-form duplex. In both B- and A-duplexes, major groove widths for the Z:P pairs are approximately 1 Å wider than those of comparable G:C pairs, perhaps to accommodate the large nitro group on Z. Otherwise, ZP-rich DNA had many of the same properties as CG-rich DNA, a conclusion supported by circular dichroism studies in solution. The ability of standard duplexes to accommodate multiple and consecutive Z:P pairs is consistent with the ability of natural polymerases to biosynthesize those pairs. This, in turn, implies that the GACTZP synthetic genetic system can explore the entire expanded sequence space that additional nucleotides create, a major step forward in this area of synthetic biology.


    Organizational Affiliation

    Biozentrum, University of Basel, 4056, Basel, Switzerland. sebastian.hiller@unibas.ch.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
reverse transcriptaseA259Moloney murine leukemia virus isolate ShinnickMutation(s): 0 
Gene Names: gag-pol
EC: 2.7.7.49 (PDB Primary Data), 2.7.7.7 (PDB Primary Data), 3.1.26.4 (PDB Primary Data), 3.4.23 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
Find proteins for P03355 (Moloney murine leukemia virus (isolate Shinnick))
Explore P03355 
Go to UniProtKB:  P03355
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 3
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(P*TP*TP*TP*AP*TP*AP*AP*G)-3')G8synthetic construct
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*CP*TP*TP*AP*TP*AP*AP*A)-3')B8synthetic construct
      Small Molecules
      Ligands 1 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      EDO
      Query on EDO

      Download CCD File 
      A
      1,2-ETHANEDIOL
      C2 H6 O2
      LYCAIKOWRPUZTN-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 1.68 Å
      • R-Value Free: 0.241 
      • R-Value Work: 0.215 
      • R-Value Observed: 0.217 
      • Space Group: P 21 21 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 54.636α = 90
      b = 145.273β = 90
      c = 46.801γ = 90
      Software Package:
      Software NamePurpose
      Aimlessdata scaling
      PHENIXrefinement
      PDB_EXTRACTdata extraction
      PHASERphasing

      Structure Validation

      View Full Validation Report



      Entry History & Funding Information

      Deposition Data


      Funding OrganizationLocationGrant Number
      National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM111386

      Revision History 

      • Version 1.0: 2015-05-27
        Type: Initial release
      • Version 1.1: 2017-01-11
        Changes: Database references
      • Version 1.2: 2017-09-20
        Changes: Author supporting evidence, Refinement description
      • Version 1.3: 2019-12-25
        Changes: Author supporting evidence, Derived calculations