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- EMDB-42009: KCTD5/Cullin3/Gbeta1gamma2 Complex State D: Reference Map for Com... -

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Basic information

Entry
Database: EMDB / ID: EMD-42009
TitleKCTD5/Cullin3/Gbeta1gamma2 Complex State D: Reference Map for Composite Map EMD-42008
Map dataKCTD5:Cullin3:GBetaGamma StateD Reference Map: Full Map
Sample
  • Complex: Complex of substrate adaptor KCTD5 with Cullin-3 and substrate Gbeta-gamma
Keywordscullin family protein / proteasome-mediated ubiquitin-dependent protein catabolic process / complex / ubiquitin-dependent protein catabolic process / CYTOSOLIC PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.98 Å
AuthorsNguyen DM / Narayanan N / Kuntz DA / Prive GG
Funding support Canada, 1 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: Structure and dynamics of a pentameric KCTD5/Cullin3/G beta gamma E3 ubiquitin ligase complex
Authors: Nguyen DM / Rath DH / Devost D / Petrin D / Rizk R / Ji AX / Narayanan N / Yong D / Zhai A / Kuntz DA / Mian MUQ / Pomroy NC / Keszei AFE / Benlekbir S / Mazhab-Jafari MT / Rubinstein JL / Hebert TE / Prive GG
#1: Journal: Biorxiv / Year: 2023
Title: Structure and dynamics of a pentameric KCTD5/Cullin3/G beta gamma E3 ubiquitin ligase complex
Authors: Nguyen DM / Rath DH / Devost D / Petrin D / Rizk R / Ji AX / Narayanan N / Yong D / Zhai A / Kuntz DA / Mian MUQ / Pomroy NC / Keszei AFE / Benlekbir S / Mazhab-Jafari MT / Rubinstein JL / Hebert TE / Prive GG
History
DepositionSep 15, 2023-
Header (metadata) releaseOct 11, 2023-
Map releaseOct 11, 2023-
UpdateApr 24, 2024-
Current statusApr 24, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42009.png

Downloads & links

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Map

FileDownload / File: emd_42009.map.gz / Format: CCP4 / Size: 129.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationKCTD5:Cullin3:GBetaGamma StateD Reference Map: Full Map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 324 pix.
= 333.72 Å		1.03 Å/pix.
x 324 pix.
= 333.72 Å		1.03 Å/pix.
x 324 pix.
= 333.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.007
Minimum - Maximum-0.016801432 - 0.07314606
Average (Standard dev.)0.00014188516 (±0.0032245484)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions324324324
Spacing324324324
CellA=B=C: 333.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_42009_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: KCTD5:Cullin3:GBetaGamma StateD Reference Map: Half Map 1

Fileemd_42009_half_map_1.map
AnnotationKCTD5:Cullin3:GBetaGamma StateD Reference Map: Half Map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: KCTD5:Cullin3:GBetaGamma StateD Reference Map: Half Map 2

Fileemd_42009_half_map_2.map
AnnotationKCTD5:Cullin3:GBetaGamma StateD Reference Map: Half Map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of substrate adaptor KCTD5 with Cullin-3 and substrate Gb...

EntireName: Complex of substrate adaptor KCTD5 with Cullin-3 and substrate Gbeta-gamma
Components
  • Complex: Complex of substrate adaptor KCTD5 with Cullin-3 and substrate Gbeta-gamma

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Supramolecule #1: Complex of substrate adaptor KCTD5 with Cullin-3 and substrate Gb...

SupramoleculeName: Complex of substrate adaptor KCTD5 with Cullin-3 and substrate Gbeta-gamma
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 / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.25 µm / Nominal magnification: 75000
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number real images: 7464 / Average electron dose: 49.35 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 4103962
Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.98 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 47975
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT

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