ISDA: 9ZQC

Deposition Date 2025-12-18

Release Date 2026-03-25

Last Version Date 2026-04-08

Entry Detail

PDB ID:

9ZQC

Keywords:

DNA BINDING PROTEIN/DNA

Title:

Nucleosome with an SSB at SHL -2.8 in complex with human PARP2 and HPF1, Class 2

Biological Source:

Source Organism(s):

Drosophila melanogaster (Taxon ID: 7227)
Mus musculus (Taxon ID: 10090)
Homo sapiens (Taxon ID: 9606)
synthetic construct (Taxon ID: 32630)

Expression System(s):

Escherichia coli

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

2.37 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Histone H2A
Gene (Uniprot):His2A, His2A:CG31618, His2A:CG33808, His2A:CG33814, His2A:CG33817, His2A:CG33820, His2A:CG33823, His2A:CG33826, His2A:CG33829, His2A:CG33832, His2A:CG33835, His2A:CG33838, His2A:CG33841, His2A:CG33844, His2A:CG33847, His2A:CG33850, His2A:CG33862, His2A:CG33865
Chain IDs:A, B
Chain Length:124
Number of Molecules:2
Biological Source:Drosophila melanogaster

UniProt ID:P84051 Pfam ID:PF00125, PF16211

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Histone H2B
Gene (Uniprot):His2B, His2B:CG17949, His2B:CG33868, His2B:CG33870, His2B:CG33872, His2B:CG33874, His2B:CG33876, His2B:CG33878, His2B:CG33880, His2B:CG33882, His2B:CG33884, His2B:CG33886, His2B:CG33888, His2B:CG33890, His2B:CG33892, His2B:CG33894, His2B:CG33896, His2B:CG33898, His2B:CG33900, His2B:CG33902, His2B:CG33904, His2B:CG33906, His2B:CG33908, His2B:CG33910
Chain IDs:C, D
Chain Length:125
Number of Molecules:2
Biological Source:Drosophila melanogaster

UniProt ID:P02283 Pfam ID:PF00125

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Histone H3
Gene (Uniprot):His3, His3:CG31613, His3:CG33803, His3:CG33806, His3:CG33809, His3:CG33812, His3:CG33815, His3:CG33818, His3:CG33821, His3:CG33824, His3:CG33827, His3:CG33830, His3:CG33833, His3:CG33836, His3:CG33839, His3:CG33842, His3:CG33845, His3:CG33848, His3:CG33851, His3:CG33854, His3:CG33857, His3:CG33860, His3:CG33863, His3:CG33866
Mutagens:C111S
Chain IDs:E, F
Chain Length:136
Number of Molecules:2
Biological Source:Drosophila melanogaster

UniProt ID:P02299 Pfam ID:PF00125

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Histone H4
Gene (Uniprot):His4, His4r, His4:CG31611, His4:CG33869, His4:CG33871, His4:CG33873, His4:CG33875, His4:CG33877, His4:CG33879, His4:CG33881, His4:CG33883, His4:CG33885, His4:CG33887, His4:CG33889, His4:CG33891, His4:CG33893, His4:CG33895, His4:CG33897, His4:CG33899, His4:CG33901, His4:CG33903, His4:CG33905, His4:CG33907, His4:CG33909
Chain IDs:G, H
Chain Length:104
Number of Molecules:2
Biological Source:Drosophila melanogaster

UniProt ID:P84040 Pfam ID:PF15511

Polymer Type:polypeptide(L)
Molecule:mAb PL2-6 antibody
Chain IDs:I, J
Chain Length:274
Number of Molecules:2
Biological Source:Mus musculus

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (60-MER)
Chain IDs:K
Chain Length:69
Number of Molecules:1
Biological Source:synthetic construct

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (128-MER)
Chain IDs:L
Chain Length:128
Number of Molecules:1
Biological Source:synthetic construct

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (197-MER)
Chain IDs:M
Chain Length:197
Number of Molecules:1
Biological Source:synthetic construct

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Poly [ADP-ribose] polymerase
Gene (Uniprot):PARP2
Chain IDs:N (auth: P)
Chain Length:494
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9UGN5 Pfam ID:PF05406, PF02877, PF00644 EC:2.4.2.30

Ligand Molecules

Primary Citation

High-Yield Production of Modified DNA Enables Structural Analysis of PARP2 Recognition of Nucleosomal Single-Strand Breaks.

Jayathilake, C, Mewhinney, C.E, Gregory-Lott, E.R, Virk, R.K, Nair, R, Yang, J, Cho, E, Day, A.G, Taylor, D.J, Kim, T.H.Show

J.Mol.Biol. 438 169753 169753 (2026)

PMID: 41819421 DOI: 10.1016/j.jmb.2026.169753

Primary Citation of related structures

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