Complex structure of DNA with self-catalyzed depurination activity

Experimental Data Snapshot

  • Resolution: 2.85 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 

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This is version 1.2 of the entry. See complete history


Crystallization and Structural Determination of 8-17 DNAzyme.

Liu, H.Mao, S.Sheng, J.Gan, J.

(2022) Methods Mol Biol 2439: 117-130

  • DOI: https://doi.org/10.1007/978-1-0716-2047-2_9
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    DNAzymes are a group of DNA molecules that can catalyze various chemical reactions. Owing to their great application potentials, DNAzymes have received significant attention. However, due to their intrinsic difficulties in crystallization and structural determination, only very limited structural information of DNAzymes is available to date. Using co-crystallization with the African Swine Fever Virus Polymerase X (AsfvPolX) protein, we have recently solved a complex structure of the 8-17 DNAzyme, which represents the first structure of the catalytically active RNA-cleaving DNAzyme. In this chapter, we describe the detailed protocols including gene construction, AsfvPolX expression and purification, crystallization, structure determination, and in vitro cleavage assay. While the specific methods described herein were originally designed for the 8-17 DNAzyme, they can also be utilized to solve other DNAzyme structures.

  • Organizational Affiliation

    Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China.


Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase beta-like protein
A, B
178African swine fever virusMutation(s): 0 
Gene Names: O174L
Find proteins for P42494 (African swine fever virus (strain Badajoz 1971 Vero-adapted))
Explore P42494 
Go to UniProtKB:  P42494
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42494
Sequence Annotations
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
D [auth b]
20synthetic construct
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.85 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 
  • Space Group: P 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.049α = 90
b = 64.544β = 90
c = 172.673γ = 90
Software Package:
Software NamePurpose
HKL-3000data reduction
PDB_EXTRACTdata extraction
HKL-3000data scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2021-08-18 
  • Deposition Author(s): Gan, J.H.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31870721

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-18
    Type: Initial release
  • Version 1.1: 2023-03-08
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description