6MIK

Crystal structure of host-guest complex with PP hachimoji DNA

• PDB DOI: https://doi.org/10.2210/pdb6MIK/pdb
• NAKB: 6MIK

• Classification: HYDROLASE/DNA
• Organism(s): Moloney murine leukemia virus isolate Shinnick, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


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

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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 

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

• PubMed: 30792304 
• DOI: https://doi.org/10.1126/science.aat0971
• Primary Citation of Related Structures:  
  6MIG, 6MIH, 6MIK


• 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 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.

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Organizational Affiliation: 

Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, No. 17, Alachua, FL 32615, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 34.31 kDa 
• Atom Count: 2,547 
• Modelled Residue Count: 264 
• Deposited Residue Count: 275 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-terminal fragment of MMLV reverse transcriptase	A	259	Moloney murine leukemia virus isolate Shinnick	Mutation(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)
UniProt
Find proteins for P03355 (Moloney murine leukemia virus (isolate Shinnick)) Explore P03355  Go to UniProtKB:  P03355

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*TP*TP*AP*TP*(1WA)P*(1WA)P*(DS))-3')	B	8	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*(DB)P*(1W5)P*(1W5)P*AP*TP*AP*AP*G)-3')	C [auth G]	8	synthetic 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 = 55.152	α = 90
b = 145.849	β = 90
c = 46.849	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• 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
• Version 1.2: 2024-03-13
  Changes: Data collection, Database references, Derived calculations