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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 / histone H3 ubiquitin ligase activity / cytoplasm organization / 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 / histone H3 ubiquitin ligase activity / cytoplasm organization / cortical granule / DNA damage sensor activity / hemi-methylated DNA-binding / homologous recombination / Signaling by BMP / protein K6-linked ubiquitination / embryonic cleavage / (E3-independent) E2 ubiquitin-conjugating enzyme / regulation of epithelial cell proliferation / intermediate filament cytoskeleton / methyl-CpG binding / histone H3K9me2/3 reader activity / protein K11-linked ubiquitination / 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 K48-linked ubiquitination / protein autoubiquitination / cis-regulatory region sequence-specific DNA binding / heterochromatin / Chromatin modifying enzymes / cytoskeleton organization / tubulin binding / epigenetic regulation of gene expression / TICAM1, RIP1-mediated IKK complex recruitment / DNA methylation / replication fork / Chromatin modifications during the maternal to zygotic transition (MZT) / IKK complex recruitment mediated by RIP1 / PINK1-PRKN Mediated Mitophagy / Negative regulators of DDX58/IFIH1 signaling / Peroxisomal protein import / protein modification process / 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 / nuclear matrix / spindle / 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: To Be Published
Title: An essential maternal PADI6-UHRF1-UBE2D (MPU) complex regulates protein ubiquitination during oocyte maturation and embryogenesis
Authors: Li J / Deng D
History
DepositionJan 25, 2025-
Header (metadata) releaseJan 28, 2026-
Map releaseJan 28, 2026-
UpdateJan 28, 2026-
Current statusJan 28, 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

Size
Brightness
Contrast
Others
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

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
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_63270_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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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