6MIK

Crystal structure of host-guest complex with PP hachimoji DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 

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
  • Structures With Same Primary Citation

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
N-terminal fragment of MMLV reverse transcriptase
A
259Moloney 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))
Go to UniProtKB:  P03355
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(P*(DB)P*(1W5)P*(1W5)P*AP*TP*AP*AP*G)-3')G8synthetic construct
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*TP*TP*AP*TP*(1WA)P*(1WA)P*(DS))-3')B8synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.152α = 90
b = 145.849β = 90
c = 46.849γ = 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