5EOS

Crystallizing Strained DNA: Self-Assembly of 3D Crystals Containing a Torsionally-Stressed Component

• PDB DOI: https://doi.org/10.2210/pdb5EOS/pdb
• NAKB: 5EOS

• Classification: DNA
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2015-11-10 Released: 2017-08-09 
• Deposition Author(s): Hernandez, C., Birktoft, J.J., Seeman, N.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 4.70 Å
• R-Value Free: 
  0.210 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Literature

Self-Assembly of 3D DNA Crystals Containing a Torsionally Stressed Component.

Hernandez, C., Birktoft, J.J., Ohayon, Y.P., Chandrasekaran, A.R., Abdallah, H., Sha, R., Stojanoff, V., Mao, C., Seeman, N.C.

(2017) Cell Chem Biol 

• PubMed: 28988948 
• DOI: https://doi.org/10.1016/j.chembiol.2017.08.018
• Primary Citation of Related Structures:  
  5EOS


• PubMed Abstract: 
  

  There is an increasing appreciation for structural diversity of DNA that is of interest to both DNA nanotechnology and basic biology. Here, we have explored how DNA responds to torsional stress by building on a previously reported two-turn DNA tensegrity triangle and demonstrating that we could introduce an extra nucleotide pair (np) into the original sequence without affecting assembly and crystallization. The extra np imposes a significant torsional stress, which is accommodated by global changes throughout the B-DNA duplex and the DNA lattice. The work reveals a near-atomic structure of naked DNA under a torsional stress of approximately 14%, and thus provides an example of DNA distortions that occur without a requirement for either an external energy source or the free energy available from protein or drug binding.

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Organizational Affiliation: 

Department of Chemistry, New York University, New York, NY 10003, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 12.8 kDa 
• Atom Count: 858 
• Modelled Residue Count: 42 
• Deposited Residue Count: 42 
• Unique nucleic acid chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*AP*GP*CP*AP*GP*CP*TP*GP*TP*G)-3')	A	11	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*AP*CP*AP*CP*CP*GP*T)-3')	B [auth D]	8	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*TP*GP*CP*TP*GP*C)-3')	C [auth B]	13	synthetic construct

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')	D [auth C]	10	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.70 Å
• R-Value Free:  0.210 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.011	α = 90
b = 110.011	β = 90
c = 83.734	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
SHELXE	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-08-09 
Deposition Author(s): Hernandez, C., Birktoft, J.J., Seeman, N.C.

Revision History  

• Version 1.0: 2017-08-09
  Type: Initial release
  
• Version 1.1: 2017-10-25
  Changes: Database references, Refinement description
• Version 1.2: 2020-06-24
  Changes: Derived calculations
• Version 1.3: 2024-03-06
  Changes: Data collection, Database references