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- EMDB-63270: Structure of human PADI6-UHRF1-UBE2D3 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-63270
TitleStructure of human PADI6-UHRF1-UBE2D3 complex
Map data
Sample
  • Complex: Heterohexamer of human PADI6-UHRF1-UBE2D3 complex
    • Protein or peptide: E3 ubiquitin-protein ligase UHRF1
    • Protein or peptide: Protein-arginine deiminase type-6
    • Protein or peptide: Ubiquitin-conjugating enzyme E2 D3
KeywordsPADI6 / UHRF1 / UBE2D3 / ubiquitylation / maternal complex / early embryonic development / LIGASE/HYDROLASE / LIGASE-HYDROLASE complex
Function / homology
Function and homology information


regulation of translation by machinery localization / protein storage / structural constituent of cytoplasmic lattice / cytoplasmic lattice / cytoplasm organization / histone H3 ubiquitin ligase activity / cortical granule / DNA damage sensor activity / hemi-methylated DNA-binding / homologous recombination ...regulation of translation by machinery localization / protein storage / structural constituent of cytoplasmic lattice / cytoplasmic lattice / cytoplasm organization / histone H3 ubiquitin ligase activity / cortical granule / DNA damage sensor activity / hemi-methylated DNA-binding / homologous recombination / Signaling by BMP / (E3-independent) E2 ubiquitin-conjugating enzyme / embryonic cleavage / protein K6-linked ubiquitination / regulation of epithelial cell proliferation / intermediate filament cytoskeleton / methyl-CpG binding / protein K11-linked ubiquitination / histone H3K9me2/3 reader activity / epigenetic programming in the zygotic pronuclei / : / : / E2 ubiquitin-conjugating enzyme / negative regulation of gene expression via chromosomal CpG island methylation / positive regulation of protein metabolic process / ubiquitin conjugating enzyme activity / mitotic spindle assembly / negative regulation of BMP signaling pathway / protein monoubiquitination / protein autoubiquitination / protein K48-linked ubiquitination / cis-regulatory region sequence-specific DNA binding / Chromatin modifying enzymes / heterochromatin / cytoskeleton organization / epigenetic regulation of gene expression / TICAM1, RIP1-mediated IKK complex recruitment / replication fork / DNA methylation / Chromatin modifications during the maternal to zygotic transition (MZT) / IKK complex recruitment mediated by RIP1 / PINK1-PRKN Mediated Mitophagy / protein modification process / Negative regulators of DDX58/IFIH1 signaling / Peroxisomal protein import / tubulin binding / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Regulation of TNFR1 signaling / euchromatin / double-strand break repair via homologous recombination / Inactivation of CSF3 (G-CSF) signaling / RING-type E3 ubiquitin transferase / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / spindle / nuclear matrix / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / heterochromatin formation / Antigen processing: Ubiquitination & Proteasome degradation / E3 ubiquitin ligases ubiquitinate target proteins / Neddylation / histone binding / ubiquitin-dependent protein catabolic process / in utero embryonic development / nucleic acid binding / proteasome-mediated ubiquitin-dependent protein catabolic process / endosome membrane / protein ubiquitination / DNA repair / apoptotic process / calcium ion binding / DNA damage response / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / extracellular exosome / zinc ion binding / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / UHRF1, tandem tudor domain / Tandem tudor domain within UHRF1 / UHRF1/2-like / Protein-arginine deiminase / Protein-arginine deiminase, C-terminal / Protein-arginine deiminase (PAD), N-terminal / Protein-arginine deiminase (PAD), central domain / Protein-arginine deiminase, central domain superfamily / PAD, N-terminal domain superfamily ...: / UHRF1, tandem tudor domain / Tandem tudor domain within UHRF1 / UHRF1/2-like / Protein-arginine deiminase / Protein-arginine deiminase, C-terminal / Protein-arginine deiminase (PAD), N-terminal / Protein-arginine deiminase (PAD), central domain / Protein-arginine deiminase, central domain superfamily / PAD, N-terminal domain superfamily / Protein-arginine deiminase (PAD) / Protein-arginine deiminase (PAD) N-terminal domain / Protein-arginine deiminase (PAD) middle domain / SRA-YDG / SRA-YDG superfamily / SAD/SRA domain / YDG domain profile. / SET and RING finger associated domain. Domain of unknown function in SET domain containing proteins and in Deinococcus radiodurans DRA1533. / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / PUA-like superfamily / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / PHD-finger / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Zinc finger PHD-type signature. / Ring finger / Cupredoxin / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger RING-type profile. / Zinc finger, RING-type / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 D3 / Inactive protein-arginine deiminase type-6 / E3 ubiquitin-protein ligase UHRF1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.03 Å
AuthorsLi J / Deng D
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31871449 China
CitationJournal: Nat Struct Mol Biol / Year: 2026
Title: The maternal PADI6-UHRF1-UBE2D complex regulates ubiquitination during oocyte maturation and embryogenesis.
Authors: Jinhong Li / Yuechao Lu / Zhili Xia / Pengliang Chi / Qianqian Qi / Sibei Liu / Sicheng Ju / Jialu Li / Zihan Zhang / Zhuo Han / Qingting Liu / Wenbo Meng / Jing Chen / Xiang Wang / Li Guo / ...Authors: Jinhong Li / Yuechao Lu / Zhili Xia / Pengliang Chi / Qianqian Qi / Sibei Liu / Sicheng Ju / Jialu Li / Zihan Zhang / Zhuo Han / Qingting Liu / Wenbo Meng / Jing Chen / Xiang Wang / Li Guo / Lei Li / Wei Huang / Lunzhi Dai / Junhong Han / Shaorong Gao / Dong Deng /
Abstract: Proteostasis in mammalian oocytes is vital for successful reproduction. The cytoplasmic lattices (CPLs) of oocytes store essential maternal proteins for early embryo development. Here we show that ...Proteostasis in mammalian oocytes is vital for successful reproduction. The cytoplasmic lattices (CPLs) of oocytes store essential maternal proteins for early embryo development. Here we show that PADI6, a core component of CPLs, forms a conserved ternary complex that we term MPU for maternal PADI6-UHRF1-UBE2D. The MPU complex regulates protein ubiquitination during oocyte maturation and early embryogenesis. We determined the cryo-electron microscopy structure of MPU and show that 86% (25/29) of clinically identified PADI6 missense variants disrupt MPU assembly, revealing a potential molecular mechanism linking dysregulation of ubiquitination on oocytes to abnormal embryonic development. Mechanistically, PADI6, with the assistance of UHRF1, sequesters UBE2D to prevent ubiquitin transfer from E2 to relevant substrate proteins, thereby suppressing the ubiquitination cascade. Therefore, our findings implicate PADI6 in the regulation of proteostasis by controlling the ubiquitination cascade, expanding our understanding of PADI6-dependent regulation of oocyte maturation and early embryogenesis.
History
DepositionJan 25, 2025-
Header (metadata) releaseJan 28, 2026-
Map releaseJan 28, 2026-
UpdateMar 11, 2026-
Current statusMar 11, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63270.png

Downloads & links

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Map

FileDownload / File: emd_63270.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 320 pix.
= 352. Å		1.1 Å/pix.
x 320 pix.
= 352. Å		1.1 Å/pix.
x 320 pix.
= 352. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-0.87776965 - 1.5668743
Average (Standard dev.)0.00062869367 (±0.040370084)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 352.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_63270_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_63270_half_map_2.map
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Sample components

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Entire : Heterohexamer of human PADI6-UHRF1-UBE2D3 complex

EntireName: Heterohexamer of human PADI6-UHRF1-UBE2D3 complex
Components
  • Complex: Heterohexamer of human PADI6-UHRF1-UBE2D3 complex
    • Protein or peptide: E3 ubiquitin-protein ligase UHRF1
    • Protein or peptide: Protein-arginine deiminase type-6
    • Protein or peptide: Ubiquitin-conjugating enzyme E2 D3

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Supramolecule #1: Heterohexamer of human PADI6-UHRF1-UBE2D3 complex

SupramoleculeName: Heterohexamer of human PADI6-UHRF1-UBE2D3 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: E3 ubiquitin-protein ligase UHRF1

MacromoleculeName: E3 ubiquitin-protein ligase UHRF1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 89.948078 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MWIQVRTMDG RQTHTVDSLS RLTKVEELRR KIQELFHVEP GLQRLFYRGK QMEDGHTLFD YEVRLNDTIQ LLVRQSLVLP HSTKERDSE LSDTDSGCCL GQSESDKSST HGEAAAETDS RPADEDMWDE TELGLYKVNE YVDARDTNMG AWFEAQVVRV T RKAPSRDE ...String:
MWIQVRTMDG RQTHTVDSLS RLTKVEELRR KIQELFHVEP GLQRLFYRGK QMEDGHTLFD YEVRLNDTIQ LLVRQSLVLP HSTKERDSE LSDTDSGCCL GQSESDKSST HGEAAAETDS RPADEDMWDE TELGLYKVNE YVDARDTNMG AWFEAQVVRV T RKAPSRDE PCSSTSRPAL EEDVIYHVKY DDYPENGVVQ MNSRDVRARA RTIIKWQDLE VGQVVMLNYN PDNPKERGFW YD AEISRKR ETRTARELYA NVVLGDDSLN DCRIIFVDEV FKIERPGEGS PMVDNPMRRK SGPSCKHCKD DVNRLCRVCA CHL CGGRQD PDKQLMCDEC DMAFHIYCLD PPLSSVPSED EWYCPECRND ASEVVLAGER LRESKKKAKM ASATSSSQRD WGKG MACVG RTKECTIVPS NHYGPIPGIP VGTMWRFRVQ VSESGVHRPH VAGIHGRSND GAYSLVLAGG YEDDVDHGNF FTYTG SGGR DLSGNKRTAE QSCDQKLTNT NRALALNCFA PINDQEGAEA KDWRSGKPVR VVRNVKGGKN SKYAPAEGNR YDGIYK VVK YWPEKGKSGF LVWRYLLRRD DDEPGPWTKE GKDRIKKLGL TMQYPEGYLE ALANREREKE NSKREEEEQQ EGGFASP RT GKGKWKRKSA GGGPSRAGSP RRTSKKTKVE PYSLTAQQSS LIREDKSNAK LWNEVLASLK DRPASGSPFQ LFLSKVEE T FQCICCQELV FRPITTVCQH NVCKDCLDRS FRAQVFSCPA CRYDLGRSYA MQVNQPLQTV LNQLFPGYGN GR

UniProtKB: E3 ubiquitin-protein ligase UHRF1

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Macromolecule #2: Protein-arginine deiminase type-6

MacromoleculeName: Protein-arginine deiminase type-6 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: protein-arginine deiminase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 77.806141 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MVSVEGRAMS FQSIIHLSLD SPVHAVCVLG TEICLDLSGC APQKCQCFTI HGSGRVLIDV ANTVISEKED ATIWWPLSDP TYATVKMTS PSPSVDADKV SVTYYGPNED APVGTAVLYL TGIEVSLEVD IYRNGQVEMS SDKQAKKKWI WGPSGWGAIL L VNCNPADV ...String:
MVSVEGRAMS FQSIIHLSLD SPVHAVCVLG TEICLDLSGC APQKCQCFTI HGSGRVLIDV ANTVISEKED ATIWWPLSDP TYATVKMTS PSPSVDADKV SVTYYGPNED APVGTAVLYL TGIEVSLEVD IYRNGQVEMS SDKQAKKKWI WGPSGWGAIL L VNCNPADV GQQLEDKKTK KVIFSEEITN LSQMTLNVQG PSCILKKYRL VLHTSKEESK KARVYWPQKD NSSTFELVLG PD QHAYTLA LLGNHLKETF YVEAIAFPSA EFSGLISYSV SLVEESQDPS IPETVLYKDT VVFRVAPCVF IPCTQVPLEV YLC RELQLQ GFVDTVTKLS EKSNSQVASV YEDPNRLGRW LQDEMAFCYT QAPHKTTSLI LDTPQAADLD EFPMKYSLSP GIGY MIQDT EDHKVASMDS IGNLMVSPPV KVQGKEYPLG RVLIGSSFYP SAEGRAMSKT LRDFLYAQQV QAPVELYSDW LMTGH VDEF MCFIPTDDKN EGKKGFLLLL ASPSACYKLF REKQKEGYGD ALLFDELRAD QLLSNGREAK TIDQLLADES LKKQNE YVE KCIHLNRDIL KTELGLVEQD IIEIPQLFCL EKLTNIPSDQ QPKRSFARPY FPDLLRMIVM GKNLGIPKPF GPQIKGT CC LEEKICCLLE PLGFKCTFIN DFDCYLTEVG DICACANIRR VPFAFKWWKM VP

UniProtKB: Inactive protein-arginine deiminase type-6

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Macromolecule #3: Ubiquitin-conjugating enzyme E2 D3

MacromoleculeName: Ubiquitin-conjugating enzyme E2 D3 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: E2 ubiquitin-conjugating enzyme
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.706133 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MALKRINKEL SDLARDPPAQ CSAGPVGDDM FHWQATIMGP NDSPYQGGVF FLTIHFPTDY PFKPPKVAFT TRIYHPNINS NGSICLDIL RSQWSPALTI SKVLLSICSL LCDPNPDDPL VPEIARIYKT DRDKYNRISR EWTQKYAM

UniProtKB: Ubiquitin-conjugating enzyme E2 D3

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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: OTHER

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 55.13 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: 1.1 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 31091
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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