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- EMDB-65291: CryoEM map of PARP10 oligomer -

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Basic information

Entry
Database: EMDB / ID: EMD-65291
TitleCryoEM map of PARP10 oligomer
Map data
Sample
  • Complex: PARP10 oligomer
    • Protein or peptide: Protein mono-ADP-ribosyltransferase PARP10
KeywordsPARP / ADP-ribosylation / condensate / oligomerization / antiviral / TRANSFERASE
Function / homology
Function and homology information


negative regulation of protein K63-linked ubiquitination / NAD+-protein-lysine ADP-ribosyltransferase activity / nicotinate metabolic process / Maturation of nucleoprotein / Nicotinate metabolism / : / protein auto-ADP-ribosylation / Maturation of nucleoprotein / K63-linked polyubiquitin modification-dependent protein binding / NAD+-protein-aspartate ADP-ribosyltransferase activity ...negative regulation of protein K63-linked ubiquitination / NAD+-protein-lysine ADP-ribosyltransferase activity / nicotinate metabolic process / Maturation of nucleoprotein / Nicotinate metabolism / : / protein auto-ADP-ribosylation / Maturation of nucleoprotein / K63-linked polyubiquitin modification-dependent protein binding / NAD+-protein-aspartate ADP-ribosyltransferase activity / protein poly-ADP-ribosylation / NAD+-protein-glutamate ADP-ribosyltransferase activity / NAD+-protein mono-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ poly-ADP-ribosyltransferase activity / negative regulation of fibroblast proliferation / nucleotidyltransferase activity / translesion synthesis / transcription corepressor activity / chromatin organization / DNA-binding transcription factor binding / viral protein processing / negative regulation of gene expression / DNA repair / nucleolus / Golgi apparatus / nucleus / cytosol / cytoplasm
Similarity search - Function
PARP-10, RNA recognition motif 1 and 2 / PARP14, third RRM domain / : / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Protein mono-ADP-ribosyltransferase PARP10
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsXu Q / Chen XX / Shi ZB
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: CryoEM structure of PARP10
Authors: Chen XX / Xu Q / Shi ZB / Yang PG
History
DepositionJul 7, 2025-
Header (metadata) releaseJul 15, 2026-
Map releaseJul 15, 2026-
UpdateJul 15, 2026-
Current statusJul 15, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65291.png

Downloads & links

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Map

FileDownload / File: emd_65291.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 400 pix.
= 368. Å		0.92 Å/pix.
x 400 pix.
= 368. Å		0.92 Å/pix.
x 400 pix.
= 368. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.92 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.62443006 - 1.1826613
Average (Standard dev.)-0.00019883501 (±0.010837395)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 368.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_65291_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_65291_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 : PARP10 oligomer

EntireName: PARP10 oligomer
Components
  • Complex: PARP10 oligomer
    • Protein or peptide: Protein mono-ADP-ribosyltransferase PARP10

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Supramolecule #1: PARP10 oligomer

SupramoleculeName: PARP10 oligomer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Protein mono-ADP-ribosyltransferase PARP10

MacromoleculeName: Protein mono-ADP-ribosyltransferase PARP10 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MVAMAEAEAG VAVEVRGLPP AVPDELLTLY FENRRRSGGG PVLSWQRLGC GGVLTFREPA DAERVLAQA DHELHGAQLS LRPAPPRAPA RLLLQGLPPG TTPQRLEQHV QALLRASGLP V QPCCALAS PRPDRALVQL PKPLSEADVR VLEEQAQNLG LEGTLVSLAR ...String:
MVAMAEAEAG VAVEVRGLPP AVPDELLTLY FENRRRSGGG PVLSWQRLGC GGVLTFREPA DAERVLAQA DHELHGAQLS LRPAPPRAPA RLLLQGLPPG TTPQRLEQHV QALLRASGLP V QPCCALAS PRPDRALVQL PKPLSEADVR VLEEQAQNLG LEGTLVSLAR VPQARAVRVV GD GASVDLL LLELYLENER RSGGGPLEDL QRLPGPLGTV ASFQQWQVAE RVLQQEHRLQ GSE LSLVPH YDILEPEELA ENTSGGDHPS TQGPRATKHA LLRTGGLVTA LQGAGTVTMG SGEE PGQSG ASLRTGPMVQ GRGIMTTGSG QEPGQSGTSL RTGPMGSLGQ AEQVSSMPMG SLEHE GLVS LRPVGLQEQE GPMSLGPVGS AGPVETSKGL LGQEGLVEIA MDSPEQEGLV GPMEIT MGS LEKAGPVSPG CVKLAGQEGL VEMVLLMEPG AMRFLQLYHE DLLAGLGDVA LLPLEGP DM TGFRLCGAQA SCQAAEEFLR SLLGSISCHV LCLEHPGSAR FLLGPEGQHL LQGLEAQF Q CVFGTERLAT ATLDTGLEEV DPTEALPVLP GNAHTLWTPD STGGDQEDVS LEEVRELLA TLEGLDLDGE DWLPRELEEE GPQEQPEEEV TPGHEEEEPV APSTVAPRWL EEEAALQLAL HRSLEPQGQ VAEQEEAAAL RQALTLSLLE QPPLEAEEPP DGGTDGKAQL VVHSAFEQDV E ELDRALRA ALEVHVQEET VGPWRRTLPA ELRARLERCH GVSVALRGDC TILRGFGAHP AR AARHLVA LLAGPWDQSL AFPLAASGPT LAGQTLKGPW NNLERLAENT GEFQEVVRAF YDT LDAARS SIRVVRVERV SHPLLQQQYE LYRERLLQRC ERRPVEQVLY HGTTAPAVPD ICAH GFNRS FCGRNATVYG KGVYFARRAS LSVQDRYSPP NADGHKAVFV ARVLTGDYGQ GRRGL RAPP LRGPGHVLLR YDSAVDCICQ PSIFVIFHDT QALPTHLITC EHVPRASPDD PSGLPG RSP DT

UniProtKB: Protein mono-ADP-ribosyltransferase PARP10

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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

Concentration0.45 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 48.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: NONE
Startup modelType of model: OTHER / Details: Ab-initial reconstruction in CryoSPARC
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 161330
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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