6MIG

Crystal structure of host-guest complex with PB hachimoji DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Hachimoji DNA and RNA: A genetic system with eight building blocks.

Hoshika, S.Leal, N.A.Kim, M.J.Kim, M.S.Karalkar, N.B.Kim, H.J.Bates, A.M.Watkins Jr., N.E.SantaLucia, H.A.Meyer, A.J.DasGupta, S.Piccirilli, J.A.Ellington, A.D.SantaLucia Jr., J.Georgiadis, M.M.Benner, S.A.

(2019) Science 363: 884-887

  • DOI: 10.1126/science.aat0971
  • Primary Citation of Related Structures:  
    6MIK, 6MIG, 6MIH

  • PubMed Abstract: 
  • We report DNA- and RNA-like systems built from eight nucleotide "letters" (hence the name "hachimoji") that form four orthogonal pairs. These synthetic systems meet the structural requirements needed to support Darwinian evolution, including a polyel ...

    We report DNA- and RNA-like systems built from eight nucleotide "letters" (hence the name "hachimoji") that form four orthogonal pairs. These synthetic systems meet the structural requirements needed to support Darwinian evolution, including a polyelectrolyte backbone, predictable thermodynamic stability, and stereoregular building blocks that fit a Schrödinger aperiodic crystal. Measured thermodynamic parameters predict the stability of hachimoji duplexes, allowing hachimoji DNA to increase the information density of natural terran DNA. Three crystal structures show that the synthetic building blocks do not perturb the aperiodic crystal seen in the DNA double helix. Hachimoji DNA was then transcribed to give hachimoji RNA in the form of a functioning fluorescent hachimoji aptamer. These results expand the scope of molecular structures that might support life, including life throughout the cosmos.


    Organizational Affiliation

    Foundation for Applied Molecular Evolution, 13709 Progress Boulevard, No. 7, Alachua, FL 32615, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Gag-Pol polyproteinA259Moloney murine leukemia virus isolate ShinnickMutation(s): 0 
Gene Names: gag-pol
EC: 3.4.23 (PDB Primary Data), 2.7.7.49 (PDB Primary Data), 2.7.7.7 (PDB Primary Data), 3.1.26.4 (PDB Primary Data), 2.7.7 (PDB Primary Data), 3.1 (PDB Primary Data)
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: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*CP*TP*TP*AP*TP*(1WA)P*(1WA)P*(DS))-3')B8synthetic construct
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(P*(DB)P*(1W5)P*(1W5)P*AP*TP*AP*AP*G)-3')G8synthetic construct
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 1.70 Å
      • R-Value Free: 0.256 
      • R-Value Work: 0.222 
      • R-Value Observed: 0.224 
      • Space Group: P 21 21 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 55.213α = 90
      b = 145.9β = 90
      c = 46.93γ = 90
      Software Package:
      Software NamePurpose
      PHENIXrefinement
      Aimlessdata scaling
      PDB_EXTRACTdata extraction
      XDSdata reduction
      PHASERphasing

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      • Deposited Date: 2018-09-19 
      • Released Date: 2019-02-27 
      • Deposition Author(s): Georgiadis, M.M.

      Revision History 

      • Version 1.0: 2019-02-27
        Type: Initial release
      • Version 1.1: 2019-03-06
        Changes: Data collection, Database references