9KZP image
Entry Detail
PDB ID:
9KZP
Keywords:
DNA/RNA
Title:
Z-form DNA-RNA hybrid in dynamic simulation
Biological Source:
Source Organism:
Homo sapiens
PDB Version:
Deposition Date:
2024-12-11
Release Date:
2024-12-25
Method Details:
Experimental Method:
SOLUTION NMR
Conformers Calculated:
50
Conformers Submitted:
10
Selection Criteria:
structures with the lowest energy
9KZP validation report
Macromolecular Entities
Polymer Type:polydeoxyribonucleotide
Description:DNA (5'-D(*(5CM)P*GP*(5CM)P*AP*(5CM)P*GP*(5CM)P*G)-3')
Chain IDs:A (auth: D)
Chain Length:8
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Description:RNA (5'-R(*CP*GP*CP*GP*UP*GP*CP*G)-3')
Chain IDs:B (auth: R)
Chain Length:8
Number of Molecules:1
Biological Source:Homo sapiens
Ligand Molecules
NA
Primary Citation
Z-form DNA-RNA hybrid blocks DNA replication.
Nucleic Acids Res. 53 ? ? (2025)
PMID: 40037715 DOI: 10.1093/nar/gkaf135

Abstact

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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Primary Citation of related structures
9KZP