ISDA: 9JVN

Deposition Date 2024-10-09

Release Date 2024-11-06

Last Version Date 2025-05-21

Entry Detail

PDB ID:

9JVN

Keywords:

DNA/RNA

Title:

Z-FORM DNA-RNA HYBRID

Biological Source:

Source Organism:

human viral metagenome (Taxon ID: 2489051)

Host Organism:

human viral metagenome

Method Details:

Experimental Method:

SOLUTION NMR

Conformers Calculated:

Conformers Submitted:

Selection Criteria:

structures with the lowest energy

Download Validation Report

Macromolecular Entities

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*CP*GP*CP*AP*CP*GP*CP*G)-3')
Chain IDs:A
Chain Length:8
Number of Molecules:1
Biological Source:human viral metagenome

Polymer Type:polyribonucleotide
Molecule:RNA (5'-R(*CP*GP*CP*GP*UP*GP*CP*G)-3')
Chain IDs:B
Chain Length:8
Number of Molecules:1
Biological Source:human viral metagenome

Ligand Molecules

Primary Citation

Z-form DNA-RNA hybrid blocks DNA replication.

Wang, S, Xu, Y.Show

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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Protein

Chemical

Disease

Primary Citation of related structures

Abstact

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