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- EMDB-60260: cryo-EM map of N8_Cullin1/Rbx1/Skp1/Skp2/Cks2/p27 in complex with... -

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Basic information

Entry
Database: EMDB / ID: EMD-60260
Titlecryo-EM map of N8_Cullin1/Rbx1/Skp1/Skp2/Cks2/p27 in complex with Extension Probe-Ub4 at a resolution of 7.05 angstrom
Map data
Sample
  • Complex: N8_Cullin1/Rbx1/Skp1/Skp2/Cks2/p27 in complex with Extension Probe-Ub4
KeywordsCullin1 / CDC34 / ubiquitin / Skp1 / Skp2 / Cks1 / LIGASE
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.05 Å
AuthorsAi HS / Liang LJ / Li CT / Zhao FY / Zhang LY / Li JH
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: cryo-EM map of N8_Cullin1/Rbx1/Skp1/Skp2/Cks2/p27 in complex with Extension Probe-Ub4 at a resolution of 7.05 angstrom
Authors: Ai HS / Liang LJ / Li CT / Zhao FY / Zhang LY / Li JH
History
DepositionMay 23, 2024-
Header (metadata) releaseMay 28, 2025-
Map releaseMay 28, 2025-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60260.png

Downloads & links

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Map

FileDownload / File: emd_60260.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.)
1.07 Å/pix.
x 256 pix.
= 274.944 Å		1.07 Å/pix.
x 256 pix.
= 274.944 Å		1.07 Å/pix.
x 256 pix.
= 274.944 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.074 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.0032816133 - 0.03433778
Average (Standard dev.)0.00019798568 (±0.0013745256)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 274.944 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_60260_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_60260_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_60260_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 : N8_Cullin1/Rbx1/Skp1/Skp2/Cks2/p27 in complex with Extension Probe-Ub4

EntireName: N8_Cullin1/Rbx1/Skp1/Skp2/Cks2/p27 in complex with Extension Probe-Ub4
Components
  • Complex: N8_Cullin1/Rbx1/Skp1/Skp2/Cks2/p27 in complex with Extension Probe-Ub4

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Supramolecule #1: N8_Cullin1/Rbx1/Skp1/Skp2/Cks2/p27 in complex with Extension Probe-Ub4

SupramoleculeName: N8_Cullin1/Rbx1/Skp1/Skp2/Cks2/p27 in complex with Extension Probe-Ub4
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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN 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 / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.05 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 45919
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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