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- EMDB-48313: PARP1 ART in complex with HPF1 and EB47 -

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Basic information

Entry
Database: EMDB / ID: EMD-48313
TitlePARP1 ART in complex with HPF1 and EB47
Map dataPARP1 ART-HPF1-EB47, non-sharpened map
Sample
  • Complex: Full-length human PARP1 bound to nicked DNA and in complex with HPF1 and Timeless fragment
    • Protein or peptide: Poly [ADP-ribose] polymerase 1
    • Protein or peptide: Histone PARylation factor 1
  • Ligand: 2-[4-[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]carbonylpiperazin-1-yl]-N-(1-oxidanylidene-2,3-dihydroisoindol-4-yl)ethanamide
KeywordsPARP1 / Zinc-finger domains / nicked DNA / DNA BINDING PROTEIN
Function / homology
Function and homology information


regulation of protein ADP-ribosylation / protein ADP-ribosyltransferase-substrate adaptor activity / NAD+-histone H2BS6 serine ADP-ribosyltransferase activity / NAD+-histone H3S10 serine ADP-ribosyltransferase activity / NAD+-histone H2BE35 glutamate ADP-ribosyltransferase activity / positive regulation of myofibroblast differentiation / negative regulation of ATP biosynthetic process / poly-ADP-D-ribose binding / NAD+-protein-tyrosine ADP-ribosyltransferase activity / NAD+-protein-histidine ADP-ribosyltransferase activity ...regulation of protein ADP-ribosylation / protein ADP-ribosyltransferase-substrate adaptor activity / NAD+-histone H2BS6 serine ADP-ribosyltransferase activity / NAD+-histone H3S10 serine ADP-ribosyltransferase activity / NAD+-histone H2BE35 glutamate ADP-ribosyltransferase activity / positive regulation of myofibroblast differentiation / negative regulation of ATP biosynthetic process / poly-ADP-D-ribose binding / NAD+-protein-tyrosine ADP-ribosyltransferase activity / NAD+-protein-histidine ADP-ribosyltransferase activity / regulation of base-excision repair / positive regulation of single strand break repair / regulation of circadian sleep/wake cycle, non-REM sleep / vRNA Synthesis / carbohydrate biosynthetic process / NAD+-protein-serine ADP-ribosyltransferase activity / negative regulation of adipose tissue development / NAD DNA ADP-ribosyltransferase activity / DNA ADP-ribosylation / mitochondrial DNA metabolic process / regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / replication fork reversal / ATP generation from poly-ADP-D-ribose / positive regulation of necroptotic process / transcription regulator activator activity / response to aldosterone / HDR through MMEJ (alt-NHEJ) / positive regulation of DNA-templated transcription, elongation / NAD+ ADP-ribosyltransferase / signal transduction involved in regulation of gene expression / protein auto-ADP-ribosylation / negative regulation of telomere maintenance via telomere lengthening / mitochondrial DNA repair / NAD+-protein-aspartate ADP-ribosyltransferase activity / protein poly-ADP-ribosylation / positive regulation of intracellular estrogen receptor signaling pathway / negative regulation of cGAS/STING signaling pathway / NAD+-protein-glutamate ADP-ribosyltransferase activity / positive regulation of cardiac muscle hypertrophy / DNA repair-dependent chromatin remodeling / cellular response to zinc ion / NAD+-protein mono-ADP-ribosyltransferase activity / positive regulation of mitochondrial depolarization / nuclear replication fork / decidualization / protein autoprocessing / R-SMAD binding / macrophage differentiation / Transferases; Glycosyltransferases; Pentosyltransferases / negative regulation of transcription elongation by RNA polymerase II / positive regulation of SMAD protein signal transduction / POLB-Dependent Long Patch Base Excision Repair / site of DNA damage / NAD+ poly-ADP-ribosyltransferase activity / SUMOylation of DNA damage response and repair proteins / positive regulation of double-strand break repair via homologous recombination / nucleosome binding / protein localization to chromatin / nucleotidyltransferase activity / transforming growth factor beta receptor signaling pathway / negative regulation of innate immune response / telomere maintenance / nuclear estrogen receptor binding / response to gamma radiation / mitochondrion organization / Downregulation of SMAD2/3:SMAD4 transcriptional activity / enzyme activator activity / protein-DNA complex / cellular response to nerve growth factor stimulus / protein modification process / DNA Damage Recognition in GG-NER / positive regulation of protein localization to nucleus / Dual Incision in GG-NER / histone deacetylase binding / cellular response to insulin stimulus / Formation of Incision Complex in GG-NER / cellular response to amyloid-beta / NAD binding / cellular response to UV / nuclear envelope / double-strand break repair / regulation of protein localization / site of double-strand break / cellular response to oxidative stress / histone binding / transcription regulator complex / damaged DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / chromosome, telomeric region / positive regulation of canonical NF-kappaB signal transduction / nuclear body / innate immune response / DNA repair / negative regulation of DNA-templated transcription / apoptotic process / DNA damage response / ubiquitin protein ligase binding / chromatin binding / protein kinase binding
Similarity search - Function
Histone PARylation factor 1 / Histone PARylation factor 1 / Poly [ADP-ribose] polymerase / PADR1 domain / PADR1 domain superfamily / : / PADR1 domain, zinc ribbon fold / PADR1, N-terminal helical domain / PADR1 domain profile. / PADR1 ...Histone PARylation factor 1 / Histone PARylation factor 1 / Poly [ADP-ribose] polymerase / PADR1 domain / PADR1 domain superfamily / : / PADR1 domain, zinc ribbon fold / PADR1, N-terminal helical domain / PADR1 domain profile. / PADR1 / Zinc finger poly(ADP-ribose) polymerase (PARP)-type signature. / Zinc finger, PARP-type superfamily / Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region / Zinc finger poly(ADP-ribose) polymerase (PARP)-type profile. / Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region / Zinc finger, PARP-type / : / 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. / BRCA1 C Terminus (BRCT) domain / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily
Similarity search - Domain/homology
Poly [ADP-ribose] polymerase 1 / Histone PARylation factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsSverzhinsky A / Pascal JM
Funding support Canada, United States, 2 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT374609 Canada
National Institutes of Health/National Cancer Institute (NIH/NCI)CA92584 United States
CitationJournal: To Be Published
Title: Structure and dynamics of PARP1-HPF1 engaging nicked DNA suggests a mechanism for acute production of localized ADP-ribose modifications
Authors: Sverzhinsky A / Xue H / Langelier M-F / Del Mundo J / Classen S / Hammel M / Rothenberg E / Pascal JM
History
DepositionDec 14, 2024-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48313.png

Downloads & links

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Map

FileDownload / File: emd_48313.map.gz / Format: CCP4 / Size: 25.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPARP1 ART-HPF1-EB47, non-sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.5 Å/pix.
x 188 pix.
= 282.752 Å		1.5 Å/pix.
x 188 pix.
= 282.752 Å		1.5 Å/pix.
x 188 pix.
= 282.752 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.504 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.4763355 - 1.0749187
Average (Standard dev.)0.00012223869 (±0.023099497)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions188188188
Spacing188188188
CellA=B=C: 282.75198 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_48313_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: PARP1 ART-HPF1-EB47, sharpened map

Fileemd_48313_additional_1.map
AnnotationPARP1 ART-HPF1-EB47, sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: PARP1 ART-HPF1-EB47, half-map A

Fileemd_48313_half_map_1.map
AnnotationPARP1 ART-HPF1-EB47, half-map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: PARP1 ART-HPF1-EB47, half-map B

Fileemd_48313_half_map_2.map
AnnotationPARP1 ART-HPF1-EB47, half-map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Full-length human PARP1 bound to nicked DNA and in complex with H...

EntireName: Full-length human PARP1 bound to nicked DNA and in complex with HPF1 and Timeless fragment
Components
  • Complex: Full-length human PARP1 bound to nicked DNA and in complex with HPF1 and Timeless fragment
    • Protein or peptide: Poly [ADP-ribose] polymerase 1
    • Protein or peptide: Histone PARylation factor 1
  • Ligand: 2-[4-[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]carbonylpiperazin-1-yl]-N-(1-oxidanylidene-2,3-dihydroisoindol-4-yl)ethanamide

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Supramolecule #1: Full-length human PARP1 bound to nicked DNA and in complex with H...

SupramoleculeName: Full-length human PARP1 bound to nicked DNA and in complex with HPF1 and Timeless fragment
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 180 KDa

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Macromolecule #1: Poly [ADP-ribose] polymerase 1

MacromoleculeName: Poly [ADP-ribose] polymerase 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: NAD+ ADP-ribosyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 115.433406 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SSGLVPRGSH MAESSDKLYR VEYAKSGRAS CKKCSESIPK DSLRMAIMVQ SPMFDGKVPH WYHFSCFWKV GHSIRHPDV EVDGFSELRW DDQQKVKKTA EAGGVTGKGQ DGIGSKAEKT LGDFAAEYAK SNRSTCKGCM EKIEKGQVRL S KKMVDPEK ...String:
MGSSHHHHHH SSGLVPRGSH MAESSDKLYR VEYAKSGRAS CKKCSESIPK DSLRMAIMVQ SPMFDGKVPH WYHFSCFWKV GHSIRHPDV EVDGFSELRW DDQQKVKKTA EAGGVTGKGQ DGIGSKAEKT LGDFAAEYAK SNRSTCKGCM EKIEKGQVRL S KKMVDPEK PQLGMIDRWY HPGCFVKNRE ELGFRPEYSA SQLKGFSLLA TEDKEALKKQ LPGVKSEGKR KGDEVDGVDE VA KKKSKKE KDKDSKLEKA LKAQNDLIWN IKDELKKVCS TNDLKELLIF NKQQVPSGES AILDRVADGM VFGALLPCEE CSG QLVFKS DAYYCTGDVT AWTKCMVKTQ TPNRKEWVTP KEFREISYLK KLKVKKQDRI FPPETSASVA ATPPPSTASA PAAV NSSAS ADKPLSNMKI LTLGKLSRNK DEVKAMIEKL GGKLTGTANK ASLCISTKKE VEKMNKKMEE VKEANIRVVS EDFLQ DVSA STKSLQELFL AHILSPWGAE VKAEPVEVVA PRGKSGAALS KKSKGQVKEE GINKSEKRMK LTLKGGAAVD PDSGLE HSA HVLEKGGKVF SATLGLVDIV KGTNSYYKLQ LLEDDKENRY WIFRSWGRVG TVIGSNKLEQ MPSKEDAIEH FMKLYEE KT GNAWHSKNFT KYPKKFYPLE IDYGQDEEAV KKLTVNPGTK SKLPKPVQDL IKMIFDVESM KKAMVEYEID LQKMPLGK L SKRQIQAAYS ILSEVQQAVS QGSSDSQILD LSNRFYTLIP HDFGMKKPPL LNNADSVQAK VEMLDNLLDI EVAYSLLRG GSDDSSKDPI DVNYEKLKTD IKVVDRDSEE AEIIRKYVKN THATTHNAYD LEVIDIFKIE REGECQRYKP FKQLHNRRLL WHGSRTTNF AGILSQGLRI APPEAPVTGY MFGKGIYFAD MVSKSANYCH TSQGDPIGLI LLGEVALGNM YELKHASHIS K LPKGKHSV KGLGKTTPDP SANISLDGVD VPLGTGISSG VNDTSLLYNE YIVYDIAQVN LKYLLKLKFN FKTSLW

UniProtKB: Poly [ADP-ribose] polymerase 1

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Macromolecule #2: Histone PARylation factor 1

MacromoleculeName: Histone PARylation factor 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.58216 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SMVGGGGKRR PGGEGPQCEK TTDVKKSKFC EADVSSDLRK EVENHYKLSL PEDFYHFWKF CEELDPEKPS DSLSASLGLQ LVGPYDILA GKHKTKKKST GLNFNLHWRF YYDPPEFQTI IIGDNKTQYH MGYFRDSPDE FPVYVGINEA KKNCIIVPNG D NVFAAVKL ...String:
SMVGGGGKRR PGGEGPQCEK TTDVKKSKFC EADVSSDLRK EVENHYKLSL PEDFYHFWKF CEELDPEKPS DSLSASLGLQ LVGPYDILA GKHKTKKKST GLNFNLHWRF YYDPPEFQTI IIGDNKTQYH MGYFRDSPDE FPVYVGINEA KKNCIIVPNG D NVFAAVKL FLTKKLREIT DKKKINLLKN IDEKLTEAAR ELGYSLEQRT VKMKQRDKKV VTKTFHGAGL VVPVDKNDVG YR ELPETDA DLKRICKTIV EAASDEERLK AFAPIQEMMT FVQFANDECD YGMGLELGMD LFCYGSHYFH KVAGQLLPLA YNL LKRNLF AEIIEEHLAN RSQENIDQLA A

UniProtKB: Histone PARylation factor 1

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Macromolecule #3: 2-[4-[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan...

MacromoleculeName: 2-[4-[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]carbonylpiperazin-1-yl]-N-(1-oxidanylidene-2,3-dihydroisoindol-4-yl)ethanamide
type: ligand / ID: 3 / Number of copies: 1 / Formula: UHB
Molecular weightTheoretical: 537.528 Da
Chemical component information

ChemComp-UHB:
2-[4-[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]carbonylpiperazin-1-yl]-N-(1-oxidanylidene-2,3-dihydroisoindol-4-yl)ethanamide

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 4246 / Average electron dose: 50.4 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 176000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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