[English] 日本語
Yorodumi
- EMDB-74602: Nucleosome with an SSB at SHL +5.3 in complex with human PARP2, H... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-74602
TitleNucleosome with an SSB at SHL +5.3 in complex with human PARP2, HPF1, and Talazoparib, Class 2, Focus map
Map datafocus map tala2
Sample
  • Complex: Nucleosome with an SSB at SHL +5.3 in complex with human PARP2, HPF1 and Talazoparib, Class 2, Focus map
KeywordsDNA damage sensing / DNA BINDING PROTEIN
Biological speciesDrosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.62 Å
AuthorsGregory-Lott E / Kim TH / Jayathilake C / Virk RK
Funding support United States, 3 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
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 19, 2025-
Header (metadata) releaseOct 14, 2026-
Map releaseOct 14, 2026-
UpdateOct 14, 2026-
Current statusOct 14, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_74602.png

Downloads & links

-
Map

FileDownload / File: emd_74602.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfocus map tala2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 400 pix.
= 331.2 Å		0.83 Å/pix.
x 400 pix.
= 331.2 Å		0.83 Å/pix.
x 400 pix.
= 331.2 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: 0.00857
Minimum - Maximum-0.2984243 - 0.7148293
Average (Standard dev.)-0.00030532572 (±0.004310636)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 331.2 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: half map A tala2 foc

Fileemd_74602_half_map_1.map
Annotationhalf map A tala2 foc
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map b tala2 foc

Fileemd_74602_half_map_2.map
Annotationhalf map b tala2 foc
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Nucleosome with an SSB at SHL +5.3 in complex with human PARP2, H...

EntireName: Nucleosome with an SSB at SHL +5.3 in complex with human PARP2, HPF1 and Talazoparib, Class 2, Focus map
Components
  • Complex: Nucleosome with an SSB at SHL +5.3 in complex with human PARP2, HPF1 and Talazoparib, Class 2, Focus map

-
Supramolecule #1: Nucleosome with an SSB at SHL +5.3 in complex with human PARP2, H...

SupramoleculeName: Nucleosome with an SSB at SHL +5.3 in complex with human PARP2, HPF1 and Talazoparib, Class 2, Focus map
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Source (natural)Organism: Drosophila melanogaster (fruit fly)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R2/1 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
SoftwareName: cryoSPARC (ver. 4.7.0)
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 49.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.7.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.62 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.0) / Number images used: 27024
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)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more