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- PDB-9ztp: Nucleosome with an SSB at SHL +5.3 in complex with human PARP2 an... -

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Basic information

Entry
Database: PDB / ID: 9ztp
TitleNucleosome with an SSB at SHL +5.3 in complex with human PARP2 and HPF1, Class 3
Components
  • DNA 130-mer
  • DNA 153-mer
  • DNA 23-mer
  • Histone H2A
  • Histone H2B
  • Histone H3
  • Histone H4
  • PL2-6 scFv
  • Poly [ADP-ribose] polymerase 2
KeywordsDNA BINDING PROTEIN/DNA / DNA damage binding protein / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


HDMs demethylate histones / PKMTs methylate histone lysines / Interleukin-7 signaling / Chromatin modifying enzymes / SUMOylation of chromatin organization proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / RMTs methylate histone arginines / E3 ubiquitin ligases ubiquitinate target proteins / RCAF complex / Factors involved in megakaryocyte development and platelet production ...HDMs demethylate histones / PKMTs methylate histone lysines / Interleukin-7 signaling / Chromatin modifying enzymes / SUMOylation of chromatin organization proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / RMTs methylate histone arginines / E3 ubiquitin ligases ubiquitinate target proteins / RCAF complex / Factors involved in megakaryocyte development and platelet production / SIRT1 negatively regulates rRNA expression / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / CHD6, CHD7, CHD8, CHD9 subfamily / polytene chromosome band / PRC2 methylates histones and DNA / Ub-specific processing proteases / Negative Regulation of CDH1 Gene Transcription / Interaction of NuRD complexes with transcription factors / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Regulation of PD-L1(CD274) transcription / larval somatic muscle development / RNA Polymerase I Promoter Escape / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Senescence-Associated Secretory Phenotype (SASP) / CHD1 and CHD2 subfamily / Regulation of endogenous retroelements by KRAB-ZFP proteins / Transcriptional regulation by small RNAs / Estrogen-dependent gene expression / Assembly of the ORC complex at the origin of replication / Oxidative Stress Induced Senescence / HATs acetylate histones / poly-ADP-D-ribose binding / polytene chromosome / NAD+-protein-serine ADP-ribosyltransferase activity / NAD DNA ADP-ribosyltransferase activity / DNA ADP-ribosylation / poly-ADP-D-ribose modification-dependent protein binding / HDR through MMEJ (alt-NHEJ) / NAD+ ADP-ribosyltransferase / protein auto-ADP-ribosylation / NAD+-protein-aspartate ADP-ribosyltransferase activity / protein poly-ADP-ribosylation / NAD+-protein-glutamate ADP-ribosyltransferase activity / decidualization / NAD+-protein mono-ADP-ribosyltransferase activity / nuclear chromosome / Transferases; Glycosyltransferases; Pentosyltransferases / POLB-Dependent Long Patch Base Excision Repair / NAD+ poly-ADP-ribosyltransferase activity / DNA repair-dependent chromatin remodeling / nucleosome binding / site of DNA damage / DNA Damage Recognition in GG-NER / Dual Incision in GG-NER / nucleosomal DNA binding / Formation of Incision Complex in GG-NER / structural constituent of chromatin / nucleosome assembly / nucleosome / chromatin organization / heterochromatin formation / damaged DNA binding / DNA repair / protein heterodimerization activity / chromosome / chromatin binding / DNA damage response / nucleolus / protein-containing complex binding / chromatin / DNA binding / nucleoplasm / nucleus
Similarity search - Function
: / Poly(ADP-ribose) polymerase, regulatory domain / WGR domain / WGR domain superfamily / WGR domain / WGR domain profile. / Proposed nucleic acid binding domain / Poly(ADP-ribose) polymerase, regulatory domain superfamily / Poly(ADP-ribose) polymerase, regulatory domain / PARP alpha-helical domain profile. ...: / Poly(ADP-ribose) polymerase, regulatory domain / WGR domain / WGR domain superfamily / WGR domain / WGR domain profile. / Proposed nucleic acid binding domain / Poly(ADP-ribose) polymerase, regulatory domain superfamily / Poly(ADP-ribose) polymerase, regulatory domain / PARP alpha-helical domain profile. / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / : / : / Histone H2A conserved site / Histone H2A signature. / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Histone H2B / Histone H3 / Histone H4 / Histone H2A / Poly [ADP-ribose] polymerase 2
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Mus musculus (house mouse)
Homo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.49 Å
AuthorsKim, T.H. / Jayathilake, C. / Virk, R.K. / Gregory-Lott, E.R.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM154859 United States
American Cancer SocietyIRG-16-186-21 United States
The G. Harold and Leila Y. Mathers Foundation2310-04968 United States
CitationJournal: Nucleic Acids Res / Year: 2026
Title: Structural basis of PARP2 recognition of nucleosomal DNA breaks and inhibitor trapping.
Authors: Chathuni Jayathilake / Emily R Gregory-Lott / Rajbinder K Virk / Grace K Koh / Eun Cho / Tae Hun Kim /
Abstract: Single-strand DNA breaks are among the most frequent forms of DNA damage, yet how PARP2 recognizes these lesions within the constrained geometry of chromatin remains unclear. Here we use cryogenic ...Single-strand DNA breaks are among the most frequent forms of DNA damage, yet how PARP2 recognizes these lesions within the constrained geometry of chromatin remains unclear. Here we use cryogenic electron microscopy (cryo-EM) to determine structures of PARP2 and HPF1 bound to nucleosomes containing a site-specific single-strand break (SSB) at superhelical location + 5.3. The structures reveal a multivalent binding mode in which the Trp-Gly-Arg (WGR) domain engages the break while the helical domain and HPF1 contact the opposing DNA gyre, spanning both DNA gyres of the nucleosome. This configuration explains the higher affinity of PARP2 for nucleosomal SSBs relative to free DNA. 3D classification resolves multiple PARP2-bound states with distinct WGR orientations and DNA backbone distortions, revealing structural plasticity during damage recognition. Comparative analysis shows that HPF1 constrains the conformational ensemble of PARP2 and promotes a defined catalytic domain architecture compatible with histone PARylation. PARP inhibitors (olaparib, talazoparib, EB-47) stabilize WGR-helical domain interfaces and make the ADP-ribosyltransferase-HPF1 catalytic module dynamic, consistent with reverse allosteric retention on damaged chromatin, while also promoting asymmetric nucleosomal DNA unwrapping. Together, these structures provide a chromatin-context framework for understanding PARP2 recognition of nucleosomal DNA breaks and how PARPis reshape these interactions to promote PARP retention and local chromatin remodeling.
History
DepositionDec 23, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 14, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone H2A
B: Histone H2A
C: Histone H2B
D: Histone H2B
E: Histone H3
F: Histone H3
G: Histone H4
H: Histone H4
I: PL2-6 scFv
J: PL2-6 scFv
K: DNA 130-mer
L: DNA 23-mer
M: DNA 153-mer
P: Poly [ADP-ribose] polymerase 2


Theoretical massNumber of molelcules
Total (without water)318,60314
Polymers318,60314
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 5 types, 9 molecules ABCDEFGHP

#1: Protein Histone H2A


Mass: 13388.727 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: His2A, H2a, His2A:CG31618, CG31618, His2A:CG33808, CG33808, His2A:CG33814, CG33814, His2A:CG33817, CG33817, His2A:CG33820, CG33820, His2A:CG33823, CG33823, His2A:CG33826, CG33826, His2A: ...Gene: His2A, H2a, His2A:CG31618, CG31618, His2A:CG33808, CG33808, His2A:CG33814, CG33814, His2A:CG33817, CG33817, His2A:CG33820, CG33820, His2A:CG33823, CG33823, His2A:CG33826, CG33826, His2A:CG33829, CG33829, His2A:CG33832, CG33832, His2A:CG33835, CG33835, His2A:CG33838, CG33838, His2A:CG33841, CG33841, His2A:CG33844, CG33844, His2A:CG33847, CG33847, His2A:CG33850, CG33850, His2A:CG33862, CG33862, His2A:CG33865, CG33865
Production host: Escherichia coli (E. coli) / References: UniProt: P84051
#2: Protein Histone H2B


Mass: 13897.275 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: His2B, His2B:CG17949, CG17949, His2B:CG33868, CG33868, His2B:CG33870, CG33870, His2B:CG33872, CG33872, His2B:CG33874, CG33874, His2B:CG33876, CG33876, His2B:CG33878, CG33878, His2B:CG33880, ...Gene: His2B, His2B:CG17949, CG17949, His2B:CG33868, CG33868, His2B:CG33870, CG33870, His2B:CG33872, CG33872, His2B:CG33874, CG33874, His2B:CG33876, CG33876, His2B:CG33878, CG33878, His2B:CG33880, CG33880, His2B:CG33882, CG33882, His2B:CG33884, CG33884, His2B:CG33886, CG33886, His2B:CG33888, CG33888, His2B:CG33890, CG33890, His2B:CG33892, CG33892, His2B:CG33894, CG33894, His2B:CG33896, CG33896, His2B:CG33898, CG33898, His2B:CG33900, CG33900, His2B:CG33902, CG33902, His2B:CG33904, CG33904, His2B:CG33906, CG33906, His2B:CG33908, CG33908, His2B:CG33910, CG33910
Production host: Escherichia coli (E. coli) / References: UniProt: P02283
#3: Protein Histone H3


Mass: 15405.036 Da / Num. of mol.: 2 / Mutation: C111S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: His3, His3:CG31613, CG31613, His3:CG33803, CG33803, His3:CG33806, CG33806, His3:CG33809, CG33809, His3:CG33812, CG33812, His3:CG33815, CG33815, His3:CG33818, CG33818, His3:CG33821, CG33821, ...Gene: His3, His3:CG31613, CG31613, His3:CG33803, CG33803, His3:CG33806, CG33806, His3:CG33809, CG33809, His3:CG33812, CG33812, His3:CG33815, CG33815, His3:CG33818, CG33818, His3:CG33821, CG33821, His3:CG33824, CG33824, His3:CG33827, CG33827, His3:CG33830, CG33830, His3:CG33833, CG33833, His3:CG33836, CG33836, His3:CG33839, CG33839, His3:CG33842, CG33842, His3:CG33845, CG33845, His3:CG33848, CG33848, His3:CG33851, CG33851, His3:CG33854, CG33854, His3:CG33857, CG33857, His3:CG33860, CG33860, His3:CG33863, CG33863, His3:CG33866, CG33866
Production host: Escherichia coli (E. coli) / References: UniProt: P02299
#4: Protein Histone H4


Mass: 11521.611 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: His4, H4, His4r, H4r, CG3379, His4:CG31611, CG31611, His4:CG33869, CG33869, His4:CG33871, CG33871, His4:CG33873, CG33873, His4:CG33875, CG33875, His4:CG33877, CG33877, His4:CG33879, CG33879, ...Gene: His4, H4, His4r, H4r, CG3379, His4:CG31611, CG31611, His4:CG33869, CG33869, His4:CG33871, CG33871, His4:CG33873, CG33873, His4:CG33875, CG33875, His4:CG33877, CG33877, His4:CG33879, CG33879, His4:CG33881, CG33881, His4:CG33883, CG33883, His4:CG33885, CG33885, His4:CG33887, CG33887, His4:CG33889, CG33889, His4:CG33891, CG33891, His4:CG33893, CG33893, His4:CG33895, CG33895, His4:CG33897, CG33897, His4:CG33899, CG33899, His4:CG33901, CG33901, His4:CG33903, CG33903, His4:CG33905, CG33905, His4:CG33907, CG33907, His4:CG33909, CG33909
Production host: Escherichia coli (E. coli) / References: UniProt: P84040
#9: Protein Poly [ADP-ribose] polymerase 2 / PARP-2 / hPARP-2 / ADP-ribosyltransferase diphtheria toxin-like 2 / ARTD2 / DNA ADP- ...PARP-2 / hPARP-2 / ADP-ribosyltransferase diphtheria toxin-like 2 / ARTD2 / DNA ADP-ribosyltransferase PARP2 / NAD(+) ADP-ribosyltransferase 2 / ADPRT-2 / Poly[ADP-ribose] synthase 2 / pADPRT-2 / Protein poly-ADP-ribosyltransferase PARP2


Mass: 56503.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARP2, ADPRT2, ADPRTL2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UGN5, NAD+ ADP-ribosyltransferase, Transferases; Glycosyltransferases; Pentosyltransferases

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DNA chain , 3 types, 3 molecules KLM

#6: DNA chain DNA 130-mer


Mass: 39859.379 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#7: DNA chain DNA 23-mer


Mass: 7054.583 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#8: DNA chain DNA 153-mer


Mass: 47497.258 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Antibody , 1 types, 2 molecules IJ

#5: Antibody PL2-6 scFv


Mass: 29631.662 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Nucleosome with an SSB at SHL +5.3 in complex with human PARP2 and HPF1
Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R2/1
VitrificationCryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 45 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.7.0particle selection
2PHENIX1.21.2_5419model refinement
5cryoSPARC4.7.0CTF correction
10cryoSPARC4.7.0initial Euler assignment
11cryoSPARC4.7.0final Euler assignment
13cryoSPARC4.7.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.49 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 90585 / Symmetry type: POINT

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