9ZQB: Nucleosome with an SSB at SHL -2.8

Nucleosome with an SSB at SHL -2.8 in complex with human PARP2 and HPF1, Class 1. Determined by electron microscopy at 2.1 Å resolution. Released 25 Mar 2026.

Method: Electron microscopy
Resolution: 2.1 Å
Organisms: Drosophila melanogaster, Mus musculus, synthetic construct
Chains: 14
Atoms: 17,106
Mol. weight: 345.8 kDa
Released: 25 Mar 2026

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

Secondary structure: helices and β-sheets

9ZQB contains 65 α-helices and 76 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: 7 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
α-helix	27-35	9
β-strand	42-43	2	1
α-helix	46-72	27
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
α-helix	117-118	2

Chain B: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
α-helix	27-36	10
β-strand	42-43	2	4
α-helix	46-72	27
β-strand	77-78	2	5
α-helix	80-88	9
α-helix	91-96	6
β-strand	100-102	3	6
α-helix	113-115	3

Chain C: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	28-32	5
α-helix	37-47	11
β-strand	52-53	2	2
α-helix	55-82	28
β-strand	87-88	2	1
α-helix	90-100	11
α-helix	103-122	20

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	103-122	20

Chain E: 6 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	38-40	3
α-helix	42-43	2
α-helix	46-57	12
α-helix	65-77	13
β-strand	84-85	2	7
α-helix	87-114	28
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	46-57	12
α-helix	65-76	12
β-strand	84-85	2	9
α-helix	87-114	28
β-strand	119-120	2	10
α-helix	122-131	10

Chain G: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	22-24	3
α-helix	27-30	4
α-helix	33-42	10
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: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	22-24	3
α-helix	27-30	4
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	98-100	3	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)
mAb PL2-6 antibody	I, J	protein	274	Mus musculus
DNA (69-mer)	K	DNA	69	synthetic construct
DNA (128-mer)	L	DNA	128	synthetic construct
DNA (197-mer)	M	DNA	197	synthetic construct
Poly [ADP-ribose] polymerase 2	P	protein	494	Homo sapiens	Q9UGN5

Sequence of entity 1 (A, B), FASTA

>9ZQB_1 Histone H2A (chains A, B)
MSGRGKGGKVKGKAKSRSNRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAA
EVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVLLPKKT
EKKA

Sequence of entity 2 (C, D), FASTA

>9ZQB_2 Histone H2B (chains C, D)
GMIPPKTSGKAAKKAGKAQKNITKTDKKKKRKRKESYAIYIYKVLKQVHPDTGISSKAMS
IMNSFVNDIFERIAAEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTK
YTSSK

Sequence of entity 3 (E, F), FASTA

>9ZQB_3 Histone H3 (chains E, F)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLSAIHAKRVTI
MPKDIQLARRIRGERA

Sequence of entity 4 (G, H), FASTA

>9ZQB_4 Histone H4 (chains G, H)
MITGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVL
KVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 5 (I, J), FASTA

>9ZQB_5 mAb PL2-6 antibody (chains I, J)
MGSSHHHHHHSSGRENLYFQGNAMDIKMTQSPSSMHASLGERVTITCKASQDIRSYLSWY
QQKPWKSPKTLIYYATSLADGVPSRFSGSGSGQDFSLTINNLESDDTATYYCLQHGESPY
TFGSGTKLEIKRAGGGGSGGGGSGGGGSGGGGSMEVQLQQSGPELVEPGTSVKMPCKASG
YTFTSYTIQWVKQTPRQGLEWIGYIYPYNAGTKYNEKFKGKATLTSDKSSSTVYMELSSL
TSEDSAVYYCARKSSRLRSTLDYWGQGTSVTVSS

Sequence of entity 6 (K), FASTA

>9ZQB_6 DNA (69-MER) (chains K)
GGACTGGACTCTATACGCGGCCATCCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGT
CGTGTCTCC

Sequence of entity 7 (L), FASTA

>9ZQB_7 DNA (128-MER) (chains L)
CTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGAT
TACTCCCTACTGACCAGGCACGTGTCAGATATATACATCCTGTGATTGTATTGAACAGCG
ACCACCCC

Sequence of entity 8 (M), FASTA

>9ZQB_8 DNA (197-MER) (chains M)
GGGGTGGTCGCTGTTCAATACAATCACAGGATGTATATATCTGACACGTGCCTGGTCAGT
AGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGG
TGCTAGAGGGAGACACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAGGATGGCCG
CGTATAGAGTCCAGTCC

Sequence of entity 9 (P), FASTA

>9ZQB_9 Poly [ADP-ribose] polymerase 2 (chains P)
GKAPVDPECTAKVGKAHVYCEGNDVYDVMLNQTNLQFNNNKYYLIQLLEDDAQRNFSVWM
RWGRVGKMGQHSLVACSGNLNKAKEIFQKKFLDKTKNNWEDREKFEKVPGKYDMLQMDYA
TNTQDEEETKKEESLKSPLKPESQLDLRVQELIKLICNVQAMEEMMMEMKYNTKKAPLGK
LTVAQIKAGYQSLKKIEDCIRAGQHGRALMEACNEFYTRIPHDFGLRTPPLIRTQKELSE
KIQLLEALGDIEIAIKLVKTELQSPEHPLDQHYRNLHCALRPLDHESYEFKVISQYLQST
HAPTHSDYTMTLLDLFEVEKDGEKEAFREDLHNRMLLWHGSRMSNWVGILSHGLRIAPPE
APITGYMFGKGIYFADMSSKSANYCFASRLKNTGLLLLSEVALGQCNELLEANPKAEGLL
QGKHSTKGLGKMAPSSAHFVTLNGSTVPLGPASDTGILNPDGYTLNYNEYIVYNPNQVRM
RYLLKVQFNFLQLW

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:

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
9ZQ9 3.3 Å, Nucleosome with an SSB at SHL -2.8 in complex with the WGR domain of human PARP2, Class 1
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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