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- EMDB-74561: Nucleosome with an SSB at SHL -2.8 in complex with the WGR domain... -

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Basic information

Entry
Database: EMDB / ID: EMD-74561
TitleNucleosome with an SSB at SHL -2.8 in complex with the WGR domain of human PARP2, Class 1
Map dataComposite map
Sample
  • Complex: Nucleosome with an SSB at SHL -2.8 in complex with the WGR domain of human PARP2
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B
    • Protein or peptide: Histone H3
    • Protein or peptide: Histone H4
    • Protein or peptide: Poly [ADP-ribose] polymerase 2
    • DNA: DNA (197-MER)
    • DNA: DNA (69-MER)
    • DNA: DNA (128-MER)
    • Protein or peptide: Ig-like domain-containing protein
KeywordsDNA 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
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsKim TH / Jayathilake C / Virk RK / Gregory-Lott ER
Funding support United States, 2 items
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: Chathuni Jayathilake / Clare E Mewhinney / Emily R Gregory-Lott / Rajbinder K Virk / Riya Nair / Junseo Yang / Eun Cho / Alexander G Day / Derek J Taylor / Tae Hun Kim /
Abstract: Preparation of high-quality nucleosomal DNA substrates in milligram quantities remains a major bottleneck for mechanistic studies of chromatin-associated processes. Here, we present an optimized ...Preparation of high-quality nucleosomal DNA substrates in milligram quantities remains a major bottleneck for mechanistic studies of chromatin-associated processes. Here, we present an optimized large-scale PCR workflow that enables rapid, low-cost production of diverse nucleosomal DNAs suitable for biochemical assays and high-resolution cryo-EM. Systematic optimization of amplification conditions yields milligram quantities of homogeneous DNA that can be fluorescently or biotin-labeled and enzymatically modified to introduce site-specific single-strand breaks (SSBs) or epigenetic marks. We also engineered an improved Nt.BsmAI nickase variant (R386D) that minimizes undesired double-strand cleavage while maintaining robust nicking activity. Using nucleosomes reconstituted with these engineered DNAs, we demonstrate the versatility of this platform across EMSA, biolayer interferometry, and cryo-EM. Structural analysis reveals how the PARP2 WGR domain engages an SSB within the nucleosome and uncovers associated shifts in H2B tail conformation that facilitate access to lesions positioned near the tail. Overall, this workflow provides a robust and scalable method for generating precisely modified nucleosomal substrates, enabling quantitative and structural dissection of PARP2-mediated DNA damage recognition and the coupled histone H2B tail rearrangements that facilitate lesion accessibility in chromatin.
History
DepositionDec 18, 2025-
Header (metadata) releaseMar 25, 2026-
Map releaseMar 25, 2026-
UpdateMar 25, 2026-
Current statusMar 25, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_74561.png

Downloads & links

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Map

FileDownload / File: emd_74561.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.91 Å/pix.
x 300 pix.
= 273. Å		0.91 Å/pix.
x 300 pix.
= 273. Å		0.91 Å/pix.
x 300 pix.
= 273. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.91 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0542
Minimum - Maximum-0.053210538 - 0.377502
Average (Standard dev.)0.0023305155 (±0.013235034)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 273.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Focused map

Fileemd_74561_additional_1.map
AnnotationFocused map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Concensus map

Fileemd_74561_additional_2.map
AnnotationConcensus map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of Composite map

Fileemd_74561_half_map_1.map
AnnotationHalf map of Composite map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of Composite map

Fileemd_74561_half_map_2.map
AnnotationHalf map of Composite map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Nucleosome with an SSB at SHL -2.8 in complex with the WGR domain...

EntireName: Nucleosome with an SSB at SHL -2.8 in complex with the WGR domain of human PARP2
Components
  • Complex: Nucleosome with an SSB at SHL -2.8 in complex with the WGR domain of human PARP2
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B
    • Protein or peptide: Histone H3
    • Protein or peptide: Histone H4
    • Protein or peptide: Poly [ADP-ribose] polymerase 2
    • DNA: DNA (197-MER)
    • DNA: DNA (69-MER)
    • DNA: DNA (128-MER)
    • Protein or peptide: Ig-like domain-containing protein

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Supramolecule #1: Nucleosome with an SSB at SHL -2.8 in complex with the WGR domain...

SupramoleculeName: Nucleosome with an SSB at SHL -2.8 in complex with the WGR domain of human PARP2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Source (natural)Organism: Drosophila melanogaster (fruit fly)

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Macromolecule #1: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 13.388727 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKGGKV KGKAKSRSNR AGLQFPVGRI HRLLRKGNYA ERVGAGAPVY LAAVMEYLAA EVLELAGNAA RDNKKTRIIP RHLQLAIRN DEELNKLLSG VTIAQGGVLP NIQAVLLPKK TEKKA

UniProtKB: Histone H2A

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Macromolecule #2: Histone H2B

MacromoleculeName: Histone H2B / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 13.897275 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GMIPPKTSGK AAKKAGKAQK NITKTDKKKK RKRKESYAIY IYKVLKQVHP DTGISSKAMS IMNSFVNDIF ERIAAEASRL AHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAVT KYTSSK

UniProtKB: Histone H2B

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Macromolecule #3: Histone H3

MacromoleculeName: Histone H3 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 15.405036 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEASEA YLVGLFEDTN LSAIHAKRVT IMPKDIQLAR RIRGERA

UniProtKB: Histone H3

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Macromolecule #4: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 11.521611 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MITGRGKGGK GLGKGGAKRH RKVLRDNIQG ITKPAIRRLA RRGGVKRISG LIYEETRGVL KVFLENVIRD AVTYTEHAKR KTVTAMDVV YALKRQGRTL YGFGG

UniProtKB: Histone H4

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Macromolecule #5: Poly [ADP-ribose] polymerase 2

MacromoleculeName: Poly [ADP-ribose] polymerase 2 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: NAD+ ADP-ribosyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.325243 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GKAPVDPECT AKVGKAHVYC EGNDVYDVML NQTNLQFNNN KYYLIQLLED DAQRNFSVWM RWGRVGKMGQ HSLVACSGNL NKAKEIFQK KFLDKTKNNW EDREKFEKVP GKYDMLQMDY ATNT

UniProtKB: Poly [ADP-ribose] polymerase 2

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Macromolecule #9: Ig-like domain-containing protein

MacromoleculeName: Ig-like domain-containing protein / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 29.631662 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SSGRENLYFQ GNAMDIKMTQ SPSSMHASLG ERVTITCKAS QDIRSYLSWY QQKPWKSPKT LIYYATSLAD GVPSRFSGS GSGQDFSLTI NNLESDDTAT YYCLQHGESP YTFGSGTKLE IKRAGGGGSG GGGSGGGGSG GGGSMEVQLQ Q SGPELVEP ...String:
MGSSHHHHHH SSGRENLYFQ GNAMDIKMTQ SPSSMHASLG ERVTITCKAS QDIRSYLSWY QQKPWKSPKT LIYYATSLAD GVPSRFSGS GSGQDFSLTI NNLESDDTAT YYCLQHGESP YTFGSGTKLE IKRAGGGGSG GGGSGGGGSG GGGSMEVQLQ Q SGPELVEP GTSVKMPCKA SGYTFTSYTI QWVKQTPRQG LEWIGYIYPY NAGTKYNEKF KGKATLTSDK SSSTVYMELS SL TSEDSAV YYCARKSSRL RSTLDYWGQG TSVTVSS

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Macromolecule #6: DNA (197-MER)

MacromoleculeName: DNA (197-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 61.197965 KDa
SequenceString: (DG)(DG)(DG)(DG)(DT)(DG)(DG)(DT)(DC)(DG) (DC)(DT)(DG)(DT)(DT)(DC)(DA)(DA)(DT)(DA) (DC)(DA)(DA)(DT)(DC)(DA)(DC)(DA)(DG) (DG)(DA)(DT)(DG)(DT)(DA)(DT)(DA)(DT)(DA) (DT) (DC)(DT)(DG)(DA)(DC)(DA) ...String:
(DG)(DG)(DG)(DG)(DT)(DG)(DG)(DT)(DC)(DG) (DC)(DT)(DG)(DT)(DT)(DC)(DA)(DA)(DT)(DA) (DC)(DA)(DA)(DT)(DC)(DA)(DC)(DA)(DG) (DG)(DA)(DT)(DG)(DT)(DA)(DT)(DA)(DT)(DA) (DT) (DC)(DT)(DG)(DA)(DC)(DA)(DC)(DG) (DT)(DG)(DC)(DC)(DT)(DG)(DG)(DT)(DC)(DA) (DG)(DT) (DA)(DG)(DG)(DG)(DA)(DG)(DT) (DA)(DA)(DT)(DC)(DC)(DC)(DC)(DT)(DT)(DG) (DG)(DC)(DG) (DG)(DT)(DT)(DA)(DA)(DA) (DA)(DC)(DG)(DC)(DG)(DG)(DG)(DG)(DG)(DA) (DC)(DA)(DG)(DC) (DG)(DC)(DG)(DT)(DA) (DC)(DG)(DT)(DG)(DC)(DG)(DT)(DT)(DT)(DA) (DA)(DG)(DC)(DG)(DG) (DT)(DG)(DC)(DT) (DA)(DG)(DA)(DG)(DG)(DG)(DA)(DG)(DA)(DC) (DA)(DC)(DG)(DA)(DC)(DC) (DA)(DA)(DT) (DT)(DG)(DA)(DG)(DC)(DG)(DG)(DC)(DC)(DT) (DC)(DG)(DG)(DC)(DA)(DC)(DC) (DG)(DG) (DG)(DA)(DT)(DT)(DC)(DT)(DC)(DC)(DA)(DG) (DG)(DA)(DT)(DG)(DG)(DC)(DC)(DG) (DC) (DG)(DT)(DA)(DT)(DA)(DG)(DA)(DG)(DT)(DC) (DC)(DA)(DG)(DT)(DC)(DC)

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Macromolecule #7: DNA (69-MER)

MacromoleculeName: DNA (69-MER) / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 21.238523 KDa
SequenceString: (DG)(DG)(DA)(DC)(DT)(DG)(DG)(DA)(DC)(DT) (DC)(DT)(DA)(DT)(DA)(DC)(DG)(DC)(DG)(DG) (DC)(DC)(DA)(DT)(DC)(DC)(DT)(DG)(DG) (DA)(DG)(DA)(DA)(DT)(DC)(DC)(DC)(DG)(DG) (DT) (DG)(DC)(DC)(DG)(DA)(DG) ...String:
(DG)(DG)(DA)(DC)(DT)(DG)(DG)(DA)(DC)(DT) (DC)(DT)(DA)(DT)(DA)(DC)(DG)(DC)(DG)(DG) (DC)(DC)(DA)(DT)(DC)(DC)(DT)(DG)(DG) (DA)(DG)(DA)(DA)(DT)(DC)(DC)(DC)(DG)(DG) (DT) (DG)(DC)(DC)(DG)(DA)(DG)(DG)(DC) (DC)(DG)(DC)(DT)(DC)(DA)(DA)(DT)(DT)(DG) (DG)(DT) (DC)(DG)(DT)(DG)(DT)(DC)(DT) (DC)(DC)

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Macromolecule #8: DNA (128-MER)

MacromoleculeName: DNA (128-MER) / type: dna / ID: 8 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 39.167 KDa
SequenceString: (DC)(DT)(DC)(DT)(DA)(DG)(DC)(DA)(DC)(DC) (DG)(DC)(DT)(DT)(DA)(DA)(DA)(DC)(DG)(DC) (DA)(DC)(DG)(DT)(DA)(DC)(DG)(DC)(DG) (DC)(DT)(DG)(DT)(DC)(DC)(DC)(DC)(DC)(DG) (DC) (DG)(DT)(DT)(DT)(DT)(DA) ...String:
(DC)(DT)(DC)(DT)(DA)(DG)(DC)(DA)(DC)(DC) (DG)(DC)(DT)(DT)(DA)(DA)(DA)(DC)(DG)(DC) (DA)(DC)(DG)(DT)(DA)(DC)(DG)(DC)(DG) (DC)(DT)(DG)(DT)(DC)(DC)(DC)(DC)(DC)(DG) (DC) (DG)(DT)(DT)(DT)(DT)(DA)(DA)(DC) (DC)(DG)(DC)(DC)(DA)(DA)(DG)(DG)(DG)(DG) (DA)(DT) (DT)(DA)(DC)(DT)(DC)(DC)(DC) (DT)(DA)(DC)(DT)(DG)(DA)(DC)(DC)(DA)(DG) (DG)(DC)(DA) (DC)(DG)(DT)(DG)(DT)(DC) (DA)(DG)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DC) (DA)(DT)(DC)(DC) (DT)(DG)(DT)(DG)(DA) (DT)(DT)(DG)(DT)(DA)(DT)(DT)(DG)(DA)(DA) (DC)(DA)(DG)(DC)(DG) (DA)(DC)(DC)(DA) (DC)(DC)(DC)(DC)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeTFS GLACIOS
SoftwareName: EPU
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 29.55 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.7.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: Alphafold model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.0) / Number images used: 50551
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.0)
FSC plot (resolution estimation)

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