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- PDB-9u4c: Structure of UBE3A dimer -

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Basic information

Entry
Database: PDB / ID: 9u4c
TitleStructure of UBE3A dimer
ComponentsIsoform I of Ubiquitin-protein ligase E3A
KeywordsLIGASE / E3 Ligase
Function / homology
Function and homology information


regulation of ubiquitin-dependent protein catabolic process / Golgi lumen acidification / HECT-type E3 ubiquitin transferase / progesterone receptor signaling pathway / response to progesterone / postsynaptic cytosol / protein autoubiquitination / protein K48-linked ubiquitination / negative regulation of TORC1 signaling / positive regulation of protein ubiquitination ...regulation of ubiquitin-dependent protein catabolic process / Golgi lumen acidification / HECT-type E3 ubiquitin transferase / progesterone receptor signaling pathway / response to progesterone / postsynaptic cytosol / protein autoubiquitination / protein K48-linked ubiquitination / negative regulation of TORC1 signaling / positive regulation of protein ubiquitination / brain development / regulation of synaptic plasticity / regulation of circadian rhythm / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / synaptic vesicle / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription coactivator activity / glutamatergic synapse / proteolysis / nucleus / cytosol / cytoplasm
Similarity search - Function
Ubiquitin-protein ligase E3A / Ubiquitin-protein ligase E3A, N-terminal zinc-binding domain / Ubiquitin-protein ligase E3A, N-terminal zinc-binding domain superfamily / Amino-terminal Zinc-binding domain of ubiquitin ligase E3A / Ubiquitin-protein ligase E3B/C / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with
Similarity search - Domain/homology
Ubiquitin-protein ligase E3A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.49 Å
AuthorsRen, X.K. / Xin, J. / Liu, J.B. / Chen, S.W. / Yan, K.G. / Liu, X.T. / Zhang, M.J.
Funding support China, 5items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82188101 China
Other government2023B0303010001
Other government2021ZT09Y104
Other governmentKQTD20210811090115021
Other governmentA2303054
CitationJournal: To Be Published
Title: Structure of UBE3A dimer
Authors: Ren, X.K. / Xin, J. / Liu, J.B. / Chen, S.W. / Yan, K.G. / Liu, X.T. / Zhang, M.J.
History
DepositionMar 19, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 23, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 23, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform I of Ubiquitin-protein ligase E3A
B: Isoform I of Ubiquitin-protein ligase E3A


Theoretical massNumber of molelcules
Total (without water)196,7722
Polymers196,7722
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1chain "A"
d_2ens_1chain "B"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: ALA / End label comp-ID: ALA / Auth seq-ID: 97 - 846 / Label seq-ID: 101 - 850

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB

NCS oper: (Code: givenMatrix: (-0.99999998024, 0.000136181548056, 0.000144825332546), (-0.000136179503836, -0.999999990628, 1.41248347977E-5), (0.000144827254731, 1.41051122767E-5, 0.999999989413) ...NCS oper: (Code: given
Matrix: (-0.99999998024, 0.000136181548056, 0.000144825332546), (-0.000136179503836, -0.999999990628, 1.41248347977E-5), (0.000144827254731, 1.41051122767E-5, 0.999999989413)
Vector: 294.356818718, 294.417129869, -0.0278897276687)

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Components

#1: Protein Isoform I of Ubiquitin-protein ligase E3A / E6AP ubiquitin-protein ligase / HECT-type ubiquitin transferase E3A / Human papillomavirus E6- ...E6AP ubiquitin-protein ligase / HECT-type ubiquitin transferase E3A / Human papillomavirus E6-associated protein / Oncogenic protein-associated protein E6-AP / Renal carcinoma antigen NY-REN-54


Mass: 98385.820 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE3A, E6AP, EPVE6AP, HPVE6A / Production host: Escherichia coli (E. coli)
References: UniProt: Q05086, HECT-type E3 ubiquitin transferase
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: UBE3A homodimer / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21-CodonPlus(DE3)-RIL
Buffer solutionpH: 7.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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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: 2200 nm / Nominal defocus min: 1200 nm / Cs: 0.007 mm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)
EM imaging opticsEnergyfilter slit width: 20 eV
Spherical aberration corrector: Microscope was modified with a Cs corrector.
Image scansWidth: 3456 / Height: 3456

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Processing

CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.49 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 180917 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 23.9 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.001711198
ELECTRON MICROSCOPYf_angle_d0.432315128
ELECTRON MICROSCOPYf_chiral_restr0.03611674
ELECTRON MICROSCOPYf_plane_restr0.00271958
ELECTRON MICROSCOPYf_dihedral_angle_d2.73741474
Refine LS restraints NCSType: NCS constraints / Rms dev position: 4.53421126621E-12 Å

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