5XK0 | pdb_00005xk0

Structure of 8-mer DNA2

• PDB DOI: https://doi.org/10.2210/pdb5XK0/pdb
• NAKB: 5XK0

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


• Deposited: 2017-05-04 Released: 2017-12-06 
• Deposition Author(s): Liu, H.H., Gan, J.H.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.196 (Depositor), 0.203 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

A DNA Structure Containing AgI -Mediated G:G and C:C Base Pairs

Liu, H.H., Shen, F.S., Haruehanroengra, P., Yao, Q.Q., Cheng, Y.S., Chen, Y.Q., Yang, C., Zhang, J., Wu, B.X., Luo, Q., Cui, R.X., Li, J.X., Ma, J.B., Sheng, J., Gan, J.H.

(2017) Angew Chem Int Ed Engl 56: 9430-9434

• PubMed: 28635152 
• DOI: https://doi.org/10.1002/anie.201704891
• Primary Citation Related Structures: 
  5XJZ, 5XK0, 5XK1


• PubMed Abstract: 
  

  Metal-mediated base pairs have been extensively utilized in many research fields, including genetic-code extension, novel therapeutics development, and nanodevice design. Compared to other cations, Ag ^I is more flexible in pairing with natural base pairs. Herein, we present a DNA structure containing two C-Ag ^I -C pairs and the first reported G-Ag ^I -G pair in a short 8mer DNA strand. This structure not only provides detailed insight into these Ag ^I -mediated base-pairing patterns in DNA, but also represents the first nonhelical DNA structure driven by heavy-metal ions, thus further contributing to the structural diversity of DNA. This unique complex structure is highly sequence-dependent, thus implying functional potentials as a new DNA aptamer that can bind and recognize silver ions. These results not only advance our understanding of the interactions between Ag ^I and nucleobases, but also provide a unique structural component for the rational design of new DNA nanodevices.

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Organizational Affiliation: 
• State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai, 200433, China.
Department of Chemistry and The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA.
State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai, 200433, China.

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 2.41 kDa 
• Atom Count: 196 
• Modeled Residue Count: 8 
• Deposited Residue Count: 8 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*CP*CP*CP*GP*AP*GP*C)-3')	A	8	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.196 (Depositor), 0.203 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.012	α = 90
b = 42.012	β = 90
c = 25.016	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-12-06 
Deposition Author(s): Liu, H.H., Gan, J.H.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31370728

Revision History  

• Version 1.0: 2017-12-06
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description