5XJZ

Structure of DNA1-Ag complex

  • Classification: DNA
  • Organism(s): synthetic construct

  • 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 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.98 Å
  • R-Value Free: 0.131 
  • R-Value Work: 0.124 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

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

  • DOI: 10.1002/anie.201704891
  • Primary Citation of Related Structures:  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, AgI is more flexible in pairing with natural base pa ...

    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, AgI is more flexible in pairing with natural base pairs. Herein, we present a DNA structure containing two C-AgI -C pairs and the first reported G-AgI -G pair in a short 8mer DNA strand. This structure not only provides detailed insight into these AgI -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 AgI and nucleobases, but also provide a unique structural component for the rational design of new DNA nanodevices.


    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*CP*AP*CP*GP*CP*GP*C)-3')A,B8synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SPM
Query on SPM

Download SDF File 
Download CCD File 
B
SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
 Ligand Interaction
AG
Query on AG

Download SDF File 
Download CCD File 
A
SILVER ION
Ag
FOIXSVOLVBLSDH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.98 Å
  • R-Value Free: 0.131 
  • R-Value Work: 0.124 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 40.236α = 90.00
b = 42.546β = 90.00
c = 25.301γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SHELXDEphasing
HKL-3000data scaling
HKL-3000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-05-04 
  • Released Date: 2017-12-06 
  • Deposition Author(s): Liu, H.H., Gan, J.H.

Funding OrganizationCountryGrant Number
National Natural Science Foundation of ChinaChina31370728

Revision History 

  • Version 1.0: 2017-12-06
    Type: Initial release