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- EMDB-63847: Mechanism of D-type cyclins recognition by the AMBRA1 E3 ligase r... -

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Basic information

Entry
Database: EMDB / ID: EMD-63847
TitleMechanism of D-type cyclins recognition by the AMBRA1 E3 ligase receptor
Map dataThe cryo-EM density map of DDB1-AMBRA1 WD40-cyclin D1 complex.
Sample
  • Complex: The complex of DDBA-AMBRA1 WD40-cyclin D1
KeywordsE3 ligase / complex / adaptor / CELL CYCLE
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.62 Å
AuthorsStjepanovic G / Wang Y
Funding support China, 1 items
OrganizationGrant numberCountry
Other government2024A1515011683 China
CitationJournal: To Be Published
Title: Mechanism of D-type cyclins recognition by the AMBRA1 E3 ligase receptor
Authors: Stjepanovic G / Wang Y
History
DepositionMar 19, 2025-
Header (metadata) releaseApr 23, 2025-
Map releaseApr 23, 2025-
UpdateApr 23, 2025-
Current statusApr 23, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63847.png

Downloads & links

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Map

FileDownload / File: emd_63847.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe cryo-EM density map of DDB1-AMBRA1 WD40-cyclin D1 complex.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 256 pix.
= 217.6 Å		0.85 Å/pix.
x 256 pix.
= 217.6 Å		0.85 Å/pix.
x 256 pix.
= 217.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.3626558 - 0.8952882
Average (Standard dev.)0.0011020409 (±0.04371144)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 217.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: The half map A of DDB1-AMBRA1 WD40-cyclin D1 complex.

Fileemd_63847_half_map_1.map
AnnotationThe half map A of DDB1-AMBRA1 WD40-cyclin D1 complex.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: The half map B of DDB1-AMBRA1 WD40-cyclin D1 complex.

Fileemd_63847_half_map_2.map
AnnotationThe half map B of DDB1-AMBRA1 WD40-cyclin D1 complex.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The complex of DDBA-AMBRA1 WD40-cyclin D1

EntireName: The complex of DDBA-AMBRA1 WD40-cyclin D1
Components
  • Complex: The complex of DDBA-AMBRA1 WD40-cyclin D1

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Supramolecule #1: The complex of DDBA-AMBRA1 WD40-cyclin D1

SupramoleculeName: The complex of DDBA-AMBRA1 WD40-cyclin D1 / type: complex / ID: 1 / Parent: 0
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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 59.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.62 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 2313103
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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