5ZU1 | pdb_00005zu1

Crystal Structure of BZ junction in diverse sequence

• PDB DOI: https://doi.org/10.2210/pdb5ZU1/pdb
• NAKB: 5ZU1

• Classification: HYDROLASE/DNA
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-05-05 Released: 2018-08-29 
• Deposition Author(s): Kim, K.K., Kim, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.01 Å
• R-Value Free: 
  0.280 (Depositor), 0.279 (DCC) 
• R-Value Work: 
  0.233 (Depositor), 0.232 (DCC) 
• R-Value Observed: 
  0.238 (Depositor) 

Starting Model: experimental

Literature

Sequence preference and structural heterogeneity of BZ junctions.

Kim, D., Hur, J., Han, J.H., Ha, S.C., Shin, D., Lee, S., Park, S., Sugiyama, H., Kim, K.K.

(2018) Nucleic Acids Res 46: 10504-10513

• PubMed: 30184200 
• DOI: https://doi.org/10.1093/nar/gky784
• Primary Citation Related Structures: 
  5ZU1, 5ZUO, 5ZUP


• PubMed Abstract: 
  

  BZ junctions, which connect B-DNA to Z-DNA, are necessary for local transformation of B-DNA to Z-DNA in the genome. However, the limited information on the junction-forming sequences and junction structures has led to a lack of understanding of the structural diversity and sequence preferences of BZ junctions. We determined three crystal structures of BZ junctions with diverse sequences followed by spectroscopic validation of DNA conformation. The structural features of the BZ junctions were well conserved regardless of sequences via the continuous base stacking through B-to-Z DNA with A-T base extrusion. However, the sequence-dependent structural heterogeneity of the junctions was also observed in base step parameters that are correlated with steric constraints imposed during Z-DNA formation. Further, circular dichroism and fluorescence-based analysis of BZ junctions revealed that a base extrusion was only found at the A-T base pair present next to a stable dinucleotide Z-DNA unit. Our findings suggest that Z-DNA formation in the genome is influenced by the sequence preference for BZ junctions.

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Organizational Affiliation: 
• Department of Molecular Cell Biology, Institute for Antimicrobial Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon 16419, Korea.
Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan.
Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Kyungbuk 37673, Korea.
Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Korea.
Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan.
Samsung Biomedical Research Institute, Samsung Advanced Institute for Health Sciences and Technology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A3B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 38.25 kDa 
• Atom Count: 2,372 
• Modeled Residue Count: 262 
• Deposited Residue Count: 286 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Double-stranded RNA-specific adenosine deaminase	A, B, C, D	63	Homo sapiens	Mutation(s): 0  Gene Names: ADAR, ADAR1, DSRAD, G1P1, IFI4 EC: 3.5.4.37
UniProt & NIH Common Fund Data Resources
Find proteins for P55265 (Homo sapiens) Explore P55265  Go to UniProtKB:  P55265
PHAROS:  P55265 GTEx:  ENSG00000160710

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*TP*CP*GP*CP*GP*CP*GP*CP*CP*TP*TP*AP*AP*AP*CP*C)-3')	E	17	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*CP*GP*GP*TP*TP*TP*AP*AP*GP*GP*CP*GP*CP*GP*CP*G)-3')	F	17	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.01 Å
• R-Value Free:  0.280 (Depositor), 0.279 (DCC) 
• R-Value Work:  0.233 (Depositor), 0.232 (DCC) 
• R-Value Observed: 0.238 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.92	α = 90
b = 108.92	β = 90
c = 62.004	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-08-29 
Deposition Author(s): Kim, K.K., Kim, D.

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Funding Organization	Location	Grant Number
	Korea, Republic Of	SSTF-BA1301-01

Revision History  

• Version 1.0: 2018-08-29
  Type: Initial release
  
• Version 1.1: 2018-09-19
  Changes: Data collection, Database references
• Version 1.2: 2018-11-21
  Changes: Data collection, Database references
• Version 1.3: 2023-11-22
  Changes: Data collection, Database references, Refinement description