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- EMDB-63840: Consensus map of UBE3A-E6-p53 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-63840
TitleConsensus map of UBE3A-E6-p53 complex
Map data
Sample
  • Complex: UBE3A-E6-p53 ternary complex
Keywordscomplex / PROTEIN BINDING
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.39 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: Consensus map of UBE3A-E6-p53 complex
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_63840.png

Downloads & links

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Map

FileDownload / File: emd_63840.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.67 Å/pix.
x 384 pix.
= 257.28 Å		0.67 Å/pix.
x 384 pix.
= 257.28 Å		0.67 Å/pix.
x 384 pix.
= 257.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.67 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.28
Minimum - Maximum-1.7074897 - 2.8420484
Average (Standard dev.)-0.00057538523 (±0.045890845)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 257.28 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_63840_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_63840_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_63840_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-E6-p53 ternary complex

EntireName: UBE3A-E6-p53 ternary complex
Components
  • Complex: UBE3A-E6-p53 ternary complex

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Supramolecule #1: UBE3A-E6-p53 ternary complex

SupramoleculeName: UBE3A-E6-p53 ternary complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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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) / 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: 2.7 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: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 111014
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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