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- PDB-9u4a: Structure of UBE3A T485E tetramer -

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Basic information

Entry
Database: PDB / ID: 9u4a
TitleStructure of UBE3A T485E tetramer
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: 3.3 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 T485E tetramer
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
C: Isoform I of Ubiquitin-protein ligase E3A
D: Isoform I of Ubiquitin-protein ligase E3A


Theoretical massNumber of molelcules
Total (without water)393,6554
Polymers393,6554
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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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: 98413.836 Da / Num. of mol.: 4 / Mutation: T485E
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 T485E homo-tetramer / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
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
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)
Image scansWidth: 5760 / Height: 4092

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Processing

CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 137906 / Symmetry type: POINT
RefinementCross valid method: NONE

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