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- EMDB-63839: Structure of UBE3A dimer -

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Basic information

Entry
Database: EMDB / ID: EMD-63839
TitleStructure of UBE3A dimer
Map data
Sample
  • Complex: UBE3A homodimer
    • Protein or peptide: Isoform I of Ubiquitin-protein ligase E3A
KeywordsE3 Ligase / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.49 Å
AuthorsRen XK / Xin J / Liu JB / Chen SW / Yan KG / Liu XT / Zhang MJ
Funding support China, 5 items
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 XK / Xin J / Liu JB / Chen SW / Yan KG / Liu XT / Zhang MJ
History
DepositionMar 19, 2025-
Header (metadata) releaseSep 23, 2026-
Map releaseSep 23, 2026-
UpdateSep 23, 2026-
Current statusSep 23, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63839.png

Downloads & links

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Map

FileDownload / File: emd_63839.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.)
0.92 Å/pix.
x 320 pix.
= 294.4 Å		0.92 Å/pix.
x 320 pix.
= 294.4 Å		0.92 Å/pix.
x 320 pix.
= 294.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.92 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-1.7664691 - 3.1344779
Average (Standard dev.)0.00034756254 (±0.057136882)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 294.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_63839_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_63839_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_63839_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : UBE3A homodimer

EntireName: UBE3A homodimer
Components
  • Complex: UBE3A homodimer
    • Protein or peptide: Isoform I of Ubiquitin-protein ligase E3A

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Supramolecule #1: UBE3A homodimer

SupramoleculeName: UBE3A homodimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Isoform I of Ubiquitin-protein ligase E3A

MacromoleculeName: Isoform I of Ubiquitin-protein ligase E3A / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: HECT-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 98.38582 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPGSMKRAAA KHLIERYYHQ LTEGCGNEAC TNEFCASCPT FLRMDNNAAA IKALELYKIN AKLCDPHPSK KGASSAYLEN SKGAPNNSC SEIKMNKKGA RIDFKDVTYL TEEKVYEILE LCREREDYSP LIRVIGRVFS SAEALVQSFR KVKQHTKEEL K SLQAKDED ...String:
GPGSMKRAAA KHLIERYYHQ LTEGCGNEAC TNEFCASCPT FLRMDNNAAA IKALELYKIN AKLCDPHPSK KGASSAYLEN SKGAPNNSC SEIKMNKKGA RIDFKDVTYL TEEKVYEILE LCREREDYSP LIRVIGRVFS SAEALVQSFR KVKQHTKEEL K SLQAKDED KDEDEKEKAA CSAAAMEEDS EASSSRIGDS SQGDNNLQKL GPDDVSVDID AIRRVYTRLL SNEKIETAFL NA LVYLSPN VECDLTYHNV YSRDPNYLNL FIIVMENRNL HSPEYLEMAL PLFCKAMSKL PLAAQGKLIR LWSKYNADQI RRM METFQQ LITYKVISNE FNSRNLVNDD DAIVAASKCL KMVYYANVVG GEVDTNHNEE DDEEPIPESS ELTLQELLGE ERRN KKGPR VDPLETELGV KTLDCRKPLI PFEEFINEPL NEVLEMDKDY TFFKVETENK FSFMTCPFIL NAVTKNLGLY YDNRI RMYS ERRITVLYSL VQGQQLNPYL RLKVRRDHII DDALVRLEMI AMENPADLKK QLYVEFEGEQ GVDEGGVSKE FFQLVV EEI FNPDIGMFTY DESTKLFWFN PSSFETEGQF TLIGIVLGLA IYNNCILDVH FPMVVYRKLM GKKGTFRDLG DSHPVLY QS LKDLLEYEGN VEDDMMITFQ ISQTDLFGNP MMYDLKENGD KIPITNENRK EFVNLYSDYI LNKSVEKQFK AFRRGFHM V TNESPLKYLF RPEEIELLIC GSRNLDFQAL EETTEYDGGY TRDSVLIREF WEIVHSFTDE QKRLFLQFTT GTDRAPVGG LGKLKMIIAK NGPDTERLPT SHTCFNVLLL PEYSSKEKLK ERLLKAITYA KGFGML

UniProtKB: Ubiquitin-protein ligase E3A

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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: 7.8
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsSpherical aberration corrector: Microscope was modified with a Cs corrector.
Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 3456 pixel / Digitization - Dimensions - Height: 3456 pixel / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.007 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.49 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 180917
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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