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- EMDB-73092: Nucleosome scFv complex with a nick at SHL +5.3 -

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Basic information

Entry
Database: EMDB / ID: EMD-73092
TitleNucleosome scFv complex with a nick at SHL +5.3
Map data
Sample
  • Complex: Nucleosome in complex with scFv20 with a nick at SHL +5.3
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B
    • Protein or peptide: Histone H3
    • Protein or peptide: Histone H4
    • Protein or peptide: scFv20
    • DNA: DNA (130-MER)
    • DNA: DNA (23-MER)
    • DNA: DNA (153-MER)
KeywordsNucleosome / Single-chain variable fragment / Nicked DNA / DNA BINDING PROTEIN
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 / polytene chromosome / nuclear chromosome / nucleosomal DNA binding / structural constituent of chromatin / nucleosome assembly / nucleosome / chromatin organization / heterochromatin formation / protein heterodimerization activity / chromosome / protein-containing complex binding / chromatin / DNA binding / nucleus
Similarity search - Function
: / : / 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 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
Similarity search - Component
Biological speciesDrosophila (fruit flies) / Drosophila melanogaster (fruit fly) / Mus musculus (house mouse) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.99 Å
AuthorsKim TH / Jayathilake C / Virk RK / Gregory-Lott ER
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM154859 United States
Other privatethe Edward Mallinckrodt, Jr. Foundation
Other privateOhio Cancer Research
American Cancer SocietyIRG-16-186-21 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
DepositionOct 9, 2025-
Header (metadata) releaseOct 14, 2026-
Map releaseOct 14, 2026-
UpdateOct 14, 2026-
Current statusOct 14, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73092.png

Downloads & links

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Map

FileDownload / File: emd_73092.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 280 pix.
= 231.84 Å		0.83 Å/pix.
x 280 pix.
= 231.84 Å		0.83 Å/pix.
x 280 pix.
= 231.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.828 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0421
Minimum - Maximum-0.3685647 - 0.7819216
Average (Standard dev.)0.00057063514 (±0.020623796)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 231.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_73092_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_73092_half_map_2.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 in complex with scFv20 with a nick at SHL +5.3

EntireName: Nucleosome in complex with scFv20 with a nick at SHL +5.3
Components
  • Complex: Nucleosome in complex with scFv20 with a nick at SHL +5.3
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B
    • Protein or peptide: Histone H3
    • Protein or peptide: Histone H4
    • Protein or peptide: scFv20
    • DNA: DNA (130-MER)
    • DNA: DNA (23-MER)
    • DNA: DNA (153-MER)

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Supramolecule #1: Nucleosome in complex with scFv20 with a nick at SHL +5.3

SupramoleculeName: Nucleosome in complex with scFv20 with a nick at SHL +5.3
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Drosophila (fruit flies)
Molecular weightTheoretical: 270 KDa

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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: scFv20

MacromoleculeName: scFv20 / type: protein_or_peptide / ID: 5 / 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 (130-MER)

MacromoleculeName: DNA (130-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 39.859379 KDa
SequenceString: (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)(DA)(DG)(DA)(DC)(DA) ...String:
(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)(DA)(DG)(DA)(DC)(DA)(DG)(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)(DT)(DC)(DT)(DC)(DC)

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Macromolecule #7: DNA (23-MER)

MacromoleculeName: DNA (23-MER) / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 7.054583 KDa
SequenceString:
(DG)(DT)(DC)(DA)(DG)(DA)(DT)(DA)(DT)(DA) (DT)(DA)(DC)(DA)(DT)(DC)(DC)(DT)(DG)(DT) (DG)(DA)(DT)

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Macromolecule #8: DNA (153-MER)

MacromoleculeName: DNA (153-MER) / type: dna / ID: 8 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 47.497258 KDa
SequenceString: (DA)(DT)(DC)(DA)(DC)(DA)(DG)(DG)(DA)(DT) (DG)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DC)(DT) (DG)(DA)(DC)(DG)(DG)(DA)(DG)(DA)(DC) (DC)(DT)(DG)(DG)(DT)(DC)(DA)(DG)(DT)(DA) (DG) (DG)(DG)(DA)(DG)(DT)(DA) ...String:
(DA)(DT)(DC)(DA)(DC)(DA)(DG)(DG)(DA)(DT) (DG)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DC)(DT) (DG)(DA)(DC)(DG)(DG)(DA)(DG)(DA)(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)(DC)(DT)(DG)(DT)(DC)(DT)(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)

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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

Concentration0.5 mg/mL
BufferpH: 7.4
Component:
ConcentrationName
10.0 mMTris
30.0 mMpotassium chloride
2.0 mMDTT
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6dzt

Final reconstructionResolution.type: BY AUTHOR / Resolution: 1.99 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.0) / Number images used: 1213156
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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