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- EMDB-63836: Cryo-EM map of UBE3A monomer -

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Basic information

Entry
Database: EMDB / ID: EMD-63836
TitleCryo-EM map of UBE3A monomer
Map data
Sample
  • Complex: UBE3A monomer
    • Protein or peptide: Ubiquitin-protein ligase E3A
KeywordsE3 Ligase / LIGASE
Function / homologyHECT-type E3 ubiquitin transferase / Isoform I of Ubiquitin-protein ligase E3A
Function and homology information
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.21 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: Cryo-EM map of UBE3A monomer
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_63836.png

Downloads & links

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Map

FileDownload / File: emd_63836.map.gz / Format: CCP4 / Size: 64 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 256 pix.
= 235.52 Å		0.92 Å/pix.
x 256 pix.
= 235.52 Å		0.92 Å/pix.
x 256 pix.
= 235.52 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: 0.22
Minimum - Maximum-2.5201678 - 2.8635445
Average (Standard dev.)-0.0005509935 (±0.049337216)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 235.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_63836_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_63836_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_63836_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 monomer

EntireName: UBE3A monomer
Components
  • Complex: UBE3A monomer
    • Protein or peptide: Ubiquitin-protein ligase E3A

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Supramolecule #1: UBE3A monomer

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

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Macromolecule #1: Ubiquitin-protein ligase E3A

MacromoleculeName: Ubiquitin-protein ligase E3A / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: HECT-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
SequenceString: GPGSMKRAAA KHLIERYYHQ LTEGCGNEAC TNEFCASCPT FLRMDNNAAA IKALELYKIN AKLCDPHPSK KGASSAYLEN SKGAPNNSCS EIKMNKKGAR IDFKDVTYLT EEKVYEILEL CREREDYSPL IRVIGRVFSS AEALVQSFRK VKQHTKEELK SLQAKDEDKD ...String:
GPGSMKRAAA KHLIERYYHQ LTEGCGNEAC TNEFCASCPT FLRMDNNAAA IKALELYKIN AKLCDPHPSK KGASSAYLEN SKGAPNNSCS EIKMNKKGAR IDFKDVTYLT EEKVYEILEL CREREDYSPL IRVIGRVFSS AEALVQSFRK VKQHTKEELK SLQAKDEDKD EDEKEKAACS AAAMEEDSEA SSSRIGDSSQ GDNNLQKLGP DDVSVDIDAI RRVYTRLLSN EKIETAFLNA LVYLSPNVEC DLTYHNVYSR DPNYLNLFII VMENRNLHSP EYLEMALPLF CKAMSKLPLA AQGKLIRLWS KYNADQIRRM METFQQLITY KVISNEFNSR NLVNDDDAIV AASKCLKMVY YANVVGGEVD TNHNEEDDEE PIPESSELTL QELLGEERRN KKGPRVDPLE TELGVKTLDC RKPLIPFEEF INEPLNEVLE MDKDYTFFKV ETENKFSFMT CPFILNAVTK NLGLYYDNRI RMYSERRITV LYSLVQGQQL NPYLRLKVRR DHIIDDALVR LEMIAMENPA DLKKQLYVEF EGEQGVDEGG VSKEFFQLVV EEIFNPDIGM FTYDESTKLF WFNPSSFETE GQFTLIGIVL GLAIYNNCIL DVHFPMVVYR KLMGKKGTFR DLGDSHPVLY QSLKDLLEYE GNVEDDMMIT FQISQTDLFG NPMMYDLKEN GDKIPITNEN RKEFVNLYSD YILNKSVEKQ FKAFRRGFHM VTNESPLKYL FRPEEIELLI CGSRNLDFQA LEETTEYDGG YTRDSVLIRE FWEIVHSFTD EQKRLFLQFT TGTDRAPVGG LGKLKMIIAK NGPDTERLPT SHTCFNVLLL PEYSSKEKLK ERLLKAITYA KGFGML

UniProtKB: Isoform I of 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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
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 / 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: 4.21 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 260131
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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