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- PDB-9zq9: Nucleosome with an SSB at SHL -2.8 in complex with the WGR domain... -

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Basic information

Entry
Database: PDB / ID: 9zq9
TitleNucleosome with an SSB at SHL -2.8 in complex with the WGR domain of human PARP2, Class 1
Components
  • DNA (128-MER)
  • DNA (197-MER)
  • DNA (69-MER)
  • Histone H2A
  • Histone H2B
  • Histone H3
  • Histone H4
  • Ig-like domain-containing protein
  • 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 / Metalloprotease DUBs / E3 ubiquitin ligases ubiquitinate target proteins / Factors involved in megakaryocyte development and platelet production / RCAF complex ...HDMs demethylate histones / PKMTs methylate histone lysines / Interleukin-7 signaling / Chromatin modifying enzymes / : / SUMOylation of chromatin organization proteins / Metalloprotease DUBs / E3 ubiquitin ligases ubiquitinate target proteins / Factors involved in megakaryocyte development and platelet production / RCAF complex / RMTs methylate histone arginines / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / SIRT1 negatively regulates rRNA expression / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / polytene chromosome band / Formation of the beta-catenin:TCF transactivating complex / Negative Regulation of CDH1 Gene Transcription / PRC2 methylates histones and DNA / HDACs deacetylate histones / Ub-specific processing proteases / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / RNA Polymerase I Promoter Escape / Regulation of endogenous retroelements by KRAB-ZFP proteins / larval somatic muscle development / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Senescence-Associated Secretory Phenotype (SASP) / Transcriptional regulation by small RNAs / Estrogen-dependent gene expression / HATs acetylate histones / response to oxygen-glucose deprivation / Assembly of the ORC complex at the origin of replication / Oxidative Stress Induced Senescence / UCH proteinases / poly-ADP-D-ribose binding / polytene chromosome / positive regulation of cell growth involved in cardiac muscle cell development / 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) / hippocampal neuron apoptotic process / NAD+ ADP-ribosyltransferase / protein auto-ADP-ribosylation / nucleosomal DNA binding / NAD+-protein-aspartate ADP-ribosyltransferase activity / protein poly-ADP-ribosylation / NAD+-protein-glutamate ADP-ribosyltransferase activity / nuclear chromosome / NAD+-protein mono-ADP-ribosyltransferase activity / DNA repair-dependent chromatin remodeling / decidualization / Transferases; Glycosyltransferases; Pentosyltransferases / POLB-Dependent Long Patch Base Excision Repair / NAD+ poly-ADP-ribosyltransferase activity / nucleosome binding / site of DNA damage / extrinsic apoptotic signaling pathway / nucleotidyltransferase activity / base-excision repair / DNA Damage Recognition in GG-NER / Dual Incision in GG-NER / Formation of Incision Complex in GG-NER / structural constituent of chromatin / nucleosome / double-strand break repair / heterochromatin formation / nucleosome assembly / chromosome / chromatin organization / damaged DNA binding / protein heterodimerization activity / DNA repair / DNA damage response / chromatin binding / chromatin / protein-containing complex binding / nucleolus / DNA binding / nucleoplasm / nucleus / cytosol
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)
Homo sapiens (human)
Mus musculus (house mouse)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsKim, T.H. / Jayathilake, C. / Virk, R.K. / Gregory-Lott, E.R.
Funding support United States, 2items
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
CitationJournal: J.Mol.Biol. / Year: 2026
Title: High-Yield Production of Modified DNA Enables Structural Analysis of PARP2 Recognition of Nucleosomal Single-Strand Breaks.
Authors: 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.
History
DepositionDec 18, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: FSC / Part number: 1 / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: FSC / Part number: 2 / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
P: Poly [ADP-ribose] polymerase 2
M: DNA (197-MER)
K: DNA (69-MER)
L: DNA (128-MER)
J: Ig-like domain-containing protein
I: Ig-like domain-containing protein


Theoretical massNumber of molelcules
Total (without water)303,61714
Polymers303,61714
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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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) / 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) / Production host: Escherichia coli (E. coli) / References: UniProt: P02283
#3: Protein Histone H3


Mass: 15405.036 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / 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) / Production host: Escherichia coli (E. coli) / References: UniProt: P84040
#5: 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: 14325.243 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 MKL

#6: DNA chain DNA (197-MER)


Mass: 61197.965 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#7: DNA chain DNA (69-MER)


Mass: 21238.523 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#8: DNA chain DNA (128-MER)


Mass: 39167.000 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Antibody , 1 types, 2 molecules JI

#9: Antibody Ig-like domain-containing protein


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 -2.8 in complex with the WGR domain of human PARP2
Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationCryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 29.55 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.7.0particle selection
2PHENIX1.21.2_5419model refinement
3EPUimage acquisition
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: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 50551 / Symmetry type: POINT
RefinementHighest resolution: 3.3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00518154
ELECTRON MICROSCOPYf_angle_d0.57125816
ELECTRON MICROSCOPYf_dihedral_angle_d26.6814882
ELECTRON MICROSCOPYf_chiral_restr0.0422881
ELECTRON MICROSCOPYf_plane_restr0.0042210

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