8YMZ | pdb_00008ymz

Structure of ZBTB43 in complex with CACA containing B-form DNA

• PDB DOI: https://doi.org/10.2210/pdb8YMZ/pdb
• NAKB: 8YMZ

• Classification: DNA/DNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-03-10 Released: 2024-10-09 
• Deposition Author(s): Li, X., Yang, Y.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 
  0.297 (Depositor), 0.299 (DCC) 
• R-Value Work: 
  0.269 (Depositor), 0.270 (DCC) 
• R-Value Observed: 
  0.272 (Depositor) 

Starting Model: in silico

Literature

Structural insights into the recognition of purine-pyrimidine dinucleotide repeats by zinc finger protein ZBTB43.

Yang, Y., Zhang, S., Xu, L., Pan, Y., Xuan, Y., Kai, Y., Chen, X.

(2024) FEBS J 291: 5002-5014

• PubMed: 39344089 
• DOI: https://doi.org/10.1111/febs.17286
• Primary Citation Related Structures: 
  8YMZ


• PubMed Abstract: 
  

  Purine-pyrimidine repeats (PPRs) can form left-handed Z-form DNA and induce DNA double-strand breaks (DSBs), posing a risk for genomic rearrangements and cancer. The zinc finger (ZF) and BTB domain-containing protein 43 (ZBTB43) is a transcription factor containing two Cys2-His2 (C2H2) and one C3H1 zinc fingers and plays a crucial role in maintaining genomic and epigenomic integrity by converting mutagenic Z-form PPRs to the B-form in prospermatogonia. Despite its importance, the molecular mechanism underlying the recognition of PPRs by ZBTB43 remains elusive. In this study, we determined the X-ray crystal structure of the ZBTB43 ZF1-3 in complex with the B-form DNA containing the CA repeats sequence. The structure reveals that ZF1 and ZF2 primarily recognize the CACA sequence through specific hydrogen-bonding and van der Waals contacts via a quadruple center involving Arg389, Met411, His413, and His414. These interactions were further validated by fluorescence-based DNA-binding assays using mutated ZBTB43 variants. Our structural investigation provides valuable insights into the recognition mechanism of PPRs by ZBTB43 and suggests a potential role for ZBTB43 in the transformation of Z-DNA to B-DNA, contributing to the maintenance of genomic stability.

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Organizational Affiliation: 
• School of Life Sciences, Anhui University, Hefei, China.
Shenzhen Medical Academy of Research and Translation (SMART), Institute of Bio-Architecture and Bio-Interactions (IBABI), China.
Faculty of Pharmaceutical Sciences, Center for Human Tissues and Organs Degeneration, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 38.04 kDa 
• Atom Count: 2,504 
• Modeled Residue Count: 218 
• Deposited Residue Count: 224 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Zinc finger and BTB domain-containing protein 43	C [auth E], F	82	Homo sapiens	Mutation(s): 0  Gene Names: ZBTB43, KIAA0414, ZBTB22B, ZNF297B
UniProt & NIH Common Fund Data Resources
Find proteins for O43298 (Homo sapiens) Explore O43298  Go to UniProtKB:  O43298
PHAROS:  O43298 GTEx:  ENSG00000169155

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*CP*AP*CP*AP*CP*AP*TP*AP*CP*AP*CP*AP*CP*T)-3')	A [auth C], D [auth A]	15	Homo sapiens

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*AP*GP*TP*GP*TP*GP*TP*AP*TP*GP*TP*GP*TP*G)-3')	B [auth D], E [auth B]	15	Homo sapiens

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	G [auth E], H [auth E], I [auth E], J [auth F], K [auth F], L [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free:  0.297 (Depositor), 0.299 (DCC) 
• R-Value Work:  0.269 (Depositor), 0.270 (DCC) 
• R-Value Observed: 0.272 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.979	α = 90
b = 67.535	β = 90
c = 99.466	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-10-09 
Deposition Author(s): Li, X., Yang, Y.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-10-09
  Type: Initial release
  
• Version 1.1: 2024-11-27
  Changes: Database references