6A85

Crystal structure of a novel DNA quadruplex

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

  • Deposited: 2018-07-06 Released: 2019-03-06 
  • 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: 1.45 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.136 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

High-resolution DNA quadruplex structure containing all the A-, G-, C-, T-tetrads.

Liu, H.H.Wang, R.Yu, X.Shen, F.S.Lan, W.X.Haruehanroengra, P.Yao, Q.Q.Zhang, J.Chen, Y.Q.Li, S.H.Wu, B.X.Zheng, L.N.Ma, J.B.Lin, J.Z.Cao, C.Y.Li, J.X.Sheng, J.Gan, J.H.

(2018) Nucleic Acids Res. 46: 11627-11638

  • DOI: 10.1093/nar/gky902

  • PubMed Abstract: 
  • DNA can form diverse structures, which predefine their physiological functions. Besides duplexes that carry the genetic information, quadruplexes are the most well-studied DNA structures. In addition to their important roles in recombination, replica ...

    DNA can form diverse structures, which predefine their physiological functions. Besides duplexes that carry the genetic information, quadruplexes are the most well-studied DNA structures. In addition to their important roles in recombination, replication, transcription and translation, DNA quadruplexes have also been applied as diagnostic aptamers and antidisease therapeutics. Herein we further expand the sequence and structure complexity of DNA quadruplex by presenting a high-resolution crystal structure of DNA1 (5'-AGAGAGATGGGTGCGTT-3'). This is the first quadruplex structure that contains all the internal A-, G-, C-, T-tetrads, A:T:A:T tetrads and bulged nucleotides in one single structure; as revealed by site-specific mutagenesis and biophysical studies, the central ATGGG motif plays important role in the quadruplex formation. Interestingly, our structure also provides great new insights into cation recognition, including the first-time reported Pb2+, by tetrad structures.


    Organizational Affiliation

    State Key Laboratory of Bioorganic and Natural Product Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Shanghai 200032, China.,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.,Department of Neurology, Huashan Hospital, Fudan University, Shanghai 200040, China.,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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*GP*AP*GP*AP*GP*AP*TP*GP*GP*GP*TP*GP*CP*GP*TP*T)-3')A,B17synthetic construct
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
LI
Query on LI

Download SDF File 
Download CCD File 
A
LITHIUM ION
Li
HBBGRARXTFLTSG-UHFFFAOYSA-N
 Ligand Interaction
PB
Query on PB

Download SDF File 
Download CCD File 
A
LEAD (II) ION
Pb
RVPVRDXYQKGNMQ-UHFFFAOYSA-N
 Ligand Interaction
NH4
Query on NH4

Download SDF File 
Download CCD File 
B
AMMONIUM ION
H4 N
QGZKDVFQNNGYKY-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.136 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 37.822α = 90.00
b = 46.651β = 90.00
c = 51.311γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL2Mapphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-07-06 
  • Released Date: 2019-03-06 
  • Deposition Author(s): Liu, H.H., Gan, J.H.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31370728

Revision History 

  • Version 1.0: 2019-03-06
    Type: Initial release