6MIK

Crystal structure of host-guest complex with PP hachimoji DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.213 

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:  

  • 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

    Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, No. 17, Alachua, FL 32615, USA. manuscripts@ffame.org.,Foundation for Applied Molecular Evolution, 13709 Progress Boulevard, No. 7, Alachua, FL 32615, USA.,DNA Software Inc., Ann Arbor, MI 48104, USA.,Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA.,Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78703, USA.,Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, No. 17, Alachua, FL 32615, USA.,Department of Biochemistry and Molecular Biology and Department of Chemistry, University of Chicago, Chicago, IL 60637, 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 Shinnick)Mutation(s): 0 
Gene Names: gag-pol
Find proteins for P03355 (Moloney murine leukemia virus (isolate Shinnick))
Go to UniProtKB:  P03355
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*TP*TP*AP*TP*(1WA)P*(1WA)P*(DS))-3')B8synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(P*(DB)P*(1W5)P*(1W5)P*AP*TP*AP*AP*G)-3')G8synthetic construct
Small Molecules
Modified Residues  4 Unique
IDChainsTypeFormula2D DiagramParent
1W5
Query on 1W5
G
DNA linkingC10 H14 N3 O9 P

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1WA
Query on 1WA
B
DNA LINKINGC10 H16 N5 O7 P

--

IGU
Query on IGU
G
DNA LINKINGC10 H14 N5 O7 PDG
JSP
Query on JSP
B
DNA linkingC10 H16 N3 O7 P

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.213 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 55.152α = 90.00
b = 145.849β = 90.00
c = 46.849γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Data collection, Database references