9KZP | pdb_00009kzp

Z-form DNA-RNA hybrid in dynamic simulation

• PDB DOI: https://doi.org/10.2210/pdb9KZP/pdb
• NAKB: 9KZP

• Classification: DNA/RNA
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2024-12-11 Released: 2024-12-25 
• Deposition Author(s): Wang, S.Y., Xu, Y.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

Z-form DNA-RNA hybrid blocks DNA replication.

Wang, S., Xu, Y.

(2025) Nucleic Acids Res 53

• PubMed: 40037715 
• DOI: https://doi.org/10.1093/nar/gkaf135
• Primary Citation of Related Structures:  
  9JVN, 9KZP


• PubMed Abstract: 
  

  We discovered that the Z-form DNA-RNA hybrid stabilized by methylated CpG repeats impacts on the initiation and elongation of Okazaki fragments, contributing to blocking DNA replication at first time. We further present the first Z-form DNA-RNA hybrid structure by using NMR spectroscopy and dynamic computation, revealing the molecular mechanism of inhibition, indicating that a distinctive zig-zag strand pattern of the Z-form hybrid with a smaller helical diameter (15 Å) and a very narrow minor groove (8.3 Å) plays the key role in the repression toward DNA replication.

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Organizational Affiliation: 
• Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan.

Biological Assembly 1  

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

Biological Assembly Evidence: NMR Distance Restraints

Macromolecule Content 

• Total Structure Weight: 5.03 kDa 
• Atom Count: 333 
• Modeled Residue Count: 16 
• Deposited Residue Count: 16 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*(5CM)P*GP*(5CM)P*AP*(5CM)P*GP*(5CM)P*G)-3')	A [auth D]	8	Homo sapiens

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*CP*GP*CP*GP*UP*GP*CP*G)-3')	B [auth R]	8	Homo sapiens

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-12-25 
Deposition Author(s): Wang, S.Y., Xu, Y.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	--

Revision History  

• Version 1.0: 2024-12-25
  Type: Initial release
  
• Version 1.1: 2025-03-19
  Changes: Database references