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- PDB-9lpk: Structure of human PADI6-UHRF1-UBE2D3 complex -

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Basic information

Entry
Database: PDB / ID: 9lpk
TitleStructure of human PADI6-UHRF1-UBE2D3 complex
Components
  • E3 ubiquitin-protein ligase UHRF1
  • Protein-arginine deiminase type-6
  • Ubiquitin-conjugating enzyme E2 D3
KeywordsLIGASE/HYDROLASE / PADI6 / UHRF1 / UBE2D3 / ubiquitylation / maternal complex / early embryonic development / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.03 Å
AuthorsLi, J. / Deng, D.
Funding support China, 1items
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, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 28, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase UHRF1
C: Protein-arginine deiminase type-6
B: Protein-arginine deiminase type-6
E: Ubiquitin-conjugating enzyme E2 D3
D: Ubiquitin-conjugating enzyme E2 D3
F: E3 ubiquitin-protein ligase UHRF1


Theoretical massNumber of molelcules
Total (without water)368,9216
Polymers368,9216
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein E3 ubiquitin-protein ligase UHRF1 / Inverted CCAAT box-binding protein of 90 kDa / Nuclear protein 95 / Nuclear zinc finger protein ...Inverted CCAAT box-binding protein of 90 kDa / Nuclear protein 95 / Nuclear zinc finger protein Np95 / HuNp95 / hNp95 / RING finger protein 106 / RING-type E3 ubiquitin transferase UHRF1 / Transcription factor ICBP90 / Ubiquitin-like PHD and RING finger domain-containing protein 1 / hUHRF1 / Ubiquitin-like-containing PHD and RING finger domains protein 1


Mass: 89948.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UHRF1, ICBP90, NP95, RNF106 / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
References: UniProt: Q96T88, RING-type E3 ubiquitin transferase
#2: Protein Protein-arginine deiminase type-6 / Peptidyl arginine deiminase-like protein / Peptidylarginine deiminase VI / hPADVI / Protein- ...Peptidyl arginine deiminase-like protein / Peptidylarginine deiminase VI / hPADVI / Protein-arginine deiminase type VI


Mass: 77806.141 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PADI6, PAD6 / Cell (production host): HEK293F / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q6TGC4, protein-arginine deiminase
#3: Protein Ubiquitin-conjugating enzyme E2 D3 / (E3-independent) E2 ubiquitin-conjugating enzyme D3 / E2 ubiquitin-conjugating enzyme D3 / ...(E3-independent) E2 ubiquitin-conjugating enzyme D3 / E2 ubiquitin-conjugating enzyme D3 / Ubiquitin carrier protein D3 / Ubiquitin-conjugating enzyme E2(17)KB 3 / Ubiquitin-conjugating enzyme E2-17 kDa 3 / Ubiquitin-protein ligase D3


Mass: 16706.133 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2D3, UBC5C, UBCH5C / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
References: UniProt: P61077, E2 ubiquitin-conjugating enzyme, (E3-independent) E2 ubiquitin-conjugating enzyme
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Heterohexamer of human PADI6-UHRF1-UBE2D3 complex / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: OTHER

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1100 nm
Image recordingElectron dose: 55.13 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487 / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 31091 / Symmetry type: POINT
RefinementHighest resolution: 3.03 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00416678
ELECTRON MICROSCOPYf_angle_d0.56122648
ELECTRON MICROSCOPYf_dihedral_angle_d3.4472235
ELECTRON MICROSCOPYf_chiral_restr0.0432481
ELECTRON MICROSCOPYf_plane_restr0.0052933

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