6QJS

Crystal structure of a DNA dodecamer containing a tetramethylpiperidinoxyl (nitroxide) spin label

• PDB DOI: https://doi.org/10.2210/pdb6QJS/pdb
• NAKB: 6QJS

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


• Deposited: 2019-01-24 Released: 2020-02-12 
• Deposition Author(s): Hardwick, J.S., Haugland, M.M., Ptchelkine, D., Brown, T., Anderson, E.E.
• Funding Organization(s): Engineering and Physical Sciences Research Council, Biotechnology and Biological Sciences Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.251 
• R-Value Work: 0.213 
• R-Value Observed: 0.215 

Literature

2'-Alkynyl spin-labelling is a minimally perturbing tool for DNA structural analysis.

Hardwick, J.S., Haugland, M.M., El-Sagheer, A.H., Ptchelkine, D., Beierlein, F.R., Lane, A.N., Brown, T., Lovett, J.E., Anderson, E.A.

(2020) Nucleic Acids Res 48: 2830-2840

• PubMed: 32052020 
• DOI: https://doi.org/10.1093/nar/gkaa086
• Primary Citation of Related Structures:  
  6QJR, 6QJS


• PubMed Abstract: 
  

  The determination of distances between specific points in nucleic acids is essential to understanding their behaviour at the molecular level. The ability to measure distances of 2-10 nm is particularly important: deformations arising from protein binding commonly fall within this range, but the reliable measurement of such distances for a conformational ensemble remains a significant challenge. Using several techniques, we show that electron paramagnetic resonance (EPR) spectroscopy of oligonucleotides spin-labelled with triazole-appended nitroxides at the 2' position offers a robust and minimally perturbing tool for obtaining such measurements. For two nitroxides, we present results from EPR spectroscopy, X-ray crystal structures of B-form spin-labelled DNA duplexes, molecular dynamics simulations and nuclear magnetic resonance spectroscopy. These four methods are mutually supportive, and pinpoint the locations of the spin labels on the duplexes. In doing so, this work establishes 2'-alkynyl nitroxide spin-labelling as a minimally perturbing method for probing DNA conformation.

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Organizational Affiliation: 

Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.

Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: mass spectrometry

Macromolecule Content

• Total Structure Weight: 8.39 kDa 
• Atom Count: 519 
• Modelled Residue Count: 22 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*CP*AP*AP*AP*TP*TP*(S6M)P*GP*CP*G)-3')	A, B	12	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NCO	C [auth A], D [auth A], E [auth A], F [auth B]	COBALT HEXAMMINE(III) Co H18 N6 DYLMFCCYOUSRTK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.251 
• R-Value Work: 0.213 
• R-Value Observed: 0.215 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.999	α = 90
b = 42.999	β = 90
c = 97.493	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-02-12 
Deposition Author(s): Hardwick, J.S., Haugland, M.M., Ptchelkine, D., Brown, T., Anderson, E.E.

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Funding Organization	Location	Grant Number
Engineering and Physical Sciences Research Council	United Kingdom	EP/M019195/1
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/J001694/1

Revision History  

• Version 1.0: 2020-02-12
  Type: Initial release
  
• Version 1.1: 2021-02-24
  Changes: Database references, Derived calculations
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description