6A85

Crystal structure of a novel DNA quadruplex

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

  • 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 
  • R-Value Observed: 0.138 

wwPDB Validation 3D Report Full Report



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
  • Structures With Same Primary Citation

  • 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 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 nucleic acids 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
PB
Query on PB

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

Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
NH4
Query on NH4

Download CCD File 
B
AMMONIUM ION
H4 N
QGZKDVFQNNGYKY-UHFFFAOYSA-O
 Ligand Interaction
LI
Query on LI

Download CCD File 
A
LITHIUM ION
Li
HBBGRARXTFLTSG-UHFFFAOYSA-N
 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 
  • R-Value Observed: 0.138 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.822α = 90
b = 46.651β = 90
c = 51.311γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
HKL2Mapphasing

Structure Validation

View Full Validation Report



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