7CPW | pdb_00007cpw

Complex structure of DNA with self-catalyzed depurination activity

• PDB DOI: https://doi.org/10.2210/pdb7CPW/pdb
• NAKB: 7CPW

• Classification: TRANSFERASE/DNA
• Organism(s): African swine fever virus, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-08-08 Released: 2021-08-18 
• Deposition Author(s): Gan, J.H.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 
  0.255 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.196 (Depositor) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

Crystallization and Structural Determination of 8-17 DNAzyme.

Liu, H., Mao, S., Sheng, J., Gan, J.

(2022) Methods Mol Biol 2439: 117-130

• PubMed: 35226319 
• DOI: https://doi.org/10.1007/978-1-0716-2047-2_9
• Primary Citation Related Structures: 
  7CPW


• 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.

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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.
Department of Chemistry and The RNA Institute, University at Albany, State University of New York, Albany, NY, USA.
Department of Chemistry and The RNA Institute, University at Albany, State University of New York, Albany, NY, USA. [e-mail].
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. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 53.59 kDa 
• Atom Count: 3,673 
• Modeled Residue Count: 390 
• Deposited Residue Count: 396 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase beta-like protein	A, B	178	African swine fever virus	Mutation(s): 0  Gene Names: O174L EC: 2.7.7.7
UniProt
Find proteins for P42494 (African swine fever virus (strain Badajoz 1971 Vero-adapted)) Explore P42494  Go to UniProtKB:  P42494

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*TP*GP*AP*TP*CP*GP*GP*AP*GP*AP*CP*GP*AP*TP*CP*AP*CP*G)-3')	C [auth a], D [auth b]	20	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free:  0.255 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.196 (Depositor) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.049	α = 90
b = 64.544	β = 90
c = 172.673	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

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

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31870721

Revision History  

• 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