9ZQ9: Nucleosome with an SSB at SHL -2.8

Nucleosome with an SSB at SHL -2.8 in complex with the WGR domain of human PARP2, Class 1. Determined by electron microscopy at 3.3 Å resolution. Released 25 Mar 2026.

Method: Electron microscopy
Resolution: 3.3 Å
Organisms: Drosophila melanogaster, Homo sapiens, synthetic construct
Chains: 14
Atoms: 17,199
Mol. weight: 303.62 kDa
Released: 25 Mar 2026

Explore 9ZQ9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9ZQ9 contains 60 α-helices and 74 β-strands across 11 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
α-helix	28-35	8
β-strand	43	1	1
α-helix	47-72	26
β-strand	77-78	2	2
α-helix	80-88	9
α-helix	91-96	6
β-strand	101-102	2	3
α-helix	113-115	3

Chain B: 7 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	12-14	3
α-helix	17-21	5
α-helix	27-36	10
β-strand	42-43	2	4
α-helix	47-72	26
β-strand	77-78	2	5
α-helix	80-88	9
α-helix	91-96	6
β-strand	101-102	2	6
α-helix	113-115	3

Chain C: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	37-45	9
β-strand	52-53	2	2
α-helix	55-82	28
β-strand	88	1	1
α-helix	90-100	11
α-helix	104-122	19

Chain D: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	29-32	4
α-helix	37-47	11
β-strand	52-53	2	5
α-helix	55-82	28
β-strand	87-88	2	4
α-helix	90-100	11
α-helix	104-123	20

Chain E: 6 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	38-40	3
α-helix	42-43	2
α-helix	47-55	9
α-helix	65-76	12
β-strand	84-85	2	7
α-helix	89-114	26
β-strand	119-120	2	8
α-helix	122-132	11

Chain F: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	42-43	2
α-helix	46-55	10
α-helix	65-79	15
β-strand	84-85	2	9
α-helix	87-114	28
β-strand	119-120	2	10
α-helix	122-131	10

Chain G: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	27-30	4
α-helix	33-43	11
β-strand	47-48	2	8
α-helix	52-77	26
β-strand	82-83	2	7
α-helix	85-94	10
β-strand	99-100	2	3

Chain H: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	28-30	3
α-helix	33-42	10
β-strand	47-48	2	10
α-helix	52-77	26
β-strand	82-83	2	9
α-helix	85-94	10
β-strand	99-100	2	6

3 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H2A	A, B	protein	124	Drosophila melanogaster	P84051 (AlphaFold model)
Histone H2B	C, D	protein	125	Drosophila melanogaster	P02283 (AlphaFold model)
Histone H3	E, F	protein	136	Drosophila melanogaster	P02299 (AlphaFold model)
Histone H4	G, H	protein	104	Drosophila melanogaster	P84040 (AlphaFold model)
Poly [ADP-ribose] polymerase 2	P	protein	123	Homo sapiens	Q9UGN5
DNA (197-mer)	M	DNA	197	synthetic construct
DNA (69-mer)	K	DNA	69	synthetic construct
DNA (128-mer)	L	DNA	128	synthetic construct
Ig-like domain-containing protein	I, J	protein	274	Mus musculus

Sequence of entity 1 (A, B), FASTA

>9ZQ9_1 Histone H2A (chains A, B)
MSGRGKGGKVKGKAKSRSNRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAA
EVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVLLPKKT
EKKA

Sequence of entity 2 (C, D), FASTA

>9ZQ9_2 Histone H2B (chains C, D)
GMIPPKTSGKAAKKAGKAQKNITKTDKKKKRKRKESYAIYIYKVLKQVHPDTGISSKAMS
IMNSFVNDIFERIAAEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTK
YTSSK

Sequence of entity 3 (E, F), FASTA

>9ZQ9_3 Histone H3 (chains E, F)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLSAIHAKRVTI
MPKDIQLARRIRGERA

Sequence of entity 4 (G, H), FASTA

>9ZQ9_4 Histone H4 (chains G, H)
MITGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVL
KVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 5 (P), FASTA

>9ZQ9_5 Poly [ADP-ribose] polymerase 2 (chains P)
GKAPVDPECTAKVGKAHVYCEGNDVYDVMLNQTNLQFNNNKYYLIQLLEDDAQRNFSVWM
RWGRVGKMGQHSLVACSGNLNKAKEIFQKKFLDKTKNNWEDREKFEKVPGKYDMLQMDYA
TNT

Sequence of entity 6 (M), FASTA

>9ZQ9_6 DNA (197-MER) (chains M)
GGGGTGGTCGCTGTTCAATACAATCACAGGATGTATATATCTGACACGTGCCTGGTCAGT
AGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGG
TGCTAGAGGGAGACACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAGGATGGCCG
CGTATAGAGTCCAGTCC

Sequence of entity 7 (K), FASTA

>9ZQ9_7 DNA (69-MER) (chains K)
GGACTGGACTCTATACGCGGCCATCCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGT
CGTGTCTCC

Sequence of entity 8 (L), FASTA

>9ZQ9_8 DNA (128-MER) (chains L)
CTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGAT
TACTCCCTACTGACCAGGCACGTGTCAGATATATACATCCTGTGATTGTATTGAACAGCG
ACCACCCC

Sequence of entity 9 (I, J), FASTA

>9ZQ9_9 Ig-like domain-containing protein (chains I, J)
MGSSHHHHHHSSGRENLYFQGNAMDIKMTQSPSSMHASLGERVTITCKASQDIRSYLSWY
QQKPWKSPKTLIYYATSLADGVPSRFSGSGSGQDFSLTINNLESDDTATYYCLQHGESPY
TFGSGTKLEIKRAGGGGSGGGGSGGGGSGGGGSMEVQLQQSGPELVEPGTSVKMPCKASG
YTFTSYTIQWVKQTPRQGLEWIGYIYPYNAGTKYNEKFKGKATLTSDKSSSTVYMELSSL
TSEDSAVYYCARKSSRLRSTLDYWGQGTSVTVSS

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. et al. J Mol Biol (2026) 438:169753-169753. DOI 10.1016/j.jmb.2026.169753 · PubMed

Other PDB entries of the same protein (UniProt P84051 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9ZQB 2.1 Å, Nucleosome with an SSB at SHL -2.8 in complex with human PARP2 and HPF1, Class 1
2NQB 2.3 Å, Drosophila Nucleosome Structure
9ZQC 2.37 Å, Nucleosome with an SSB at SHL -2.8 in complex with human PARP2 and HPF1, Class 2
2PYO 2.43 Å, Drosophila nucleosome core
8UX1 2.5 Å, Cryo-EM structure of Ran bound to RCC1 and the nucleosome core particle
8PP7 2.91 Å, human RYBP-PRC1 bound to mononucleosome
6DZT 2.99 Å, Cryo-EM structure of nucleosome in complex with a single chain antibody fragment
8PP6 3.18 Å, human RYBP-PRC1 bound to H2AK118ub1 nucleosome
9ZQA 3.28 Å, Nucleosome with an SSB at SHL -2.8 in complex with the WGR domain of human PARP2, Class 2
9MU4 3.29 Å, Structure of a native Drosophila melanogaster octameric nucleosome
4X23 3.5 Å, Crystal structure of cenp-C in complex with the nucleosome core particle
4QLC 3.5 Å, Crystal structure of chromatosome at 3.5 angstrom resolution

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