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- EMDB-14558: Structure of the CUL7-RBX1-FBXW8-SKP1-CUL1 N-terminal region form... -

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Basic information

Entry
Database: EMDB / ID: EMD-14558
TitleStructure of the CUL7-RBX1-FBXW8-SKP1-CUL1 N-terminal region forming multi cullin-RING ligase complex
Map data
Sample
  • Complex: Structure of the CUL7-RBX1-FBXW8-SKP1-CUL1 N-terminal region forming multi cullin-RING ligase complex
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.4 Å
AuthorsHopf LVM / Schulman BA
Funding supportEuropean Union, Germany, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)789016European Union
Max Planck Society Germany
CitationJournal: Nat Struct Mol Biol / Year: 2022
Title: Structure of CRL7 reveals coupling with CUL1-RBX1/ROC1 for multi-cullin-RING E3-catalyzed ubiquitin ligation.
Authors: Linus V M Hopf / Kheewoong Baek / Maren Klügel / Susanne von Gronau / Yue Xiong / Brenda A Schulman /
Abstract: Most cullin-RING ubiquitin ligases (CRLs) form homologous assemblies between a neddylated cullin-RING catalytic module and a variable substrate-binding receptor (for example, an F-box protein). ...Most cullin-RING ubiquitin ligases (CRLs) form homologous assemblies between a neddylated cullin-RING catalytic module and a variable substrate-binding receptor (for example, an F-box protein). However, the vertebrate-specific CRL7 is of interest because it eludes existing models, yet its constituent cullin CUL7 and F-box protein FBXW8 are essential for development, and CUL7 mutations cause 3M syndrome. In this study, cryo-EM and biochemical analyses reveal the CRL7 assembly. CUL7's exclusivity for FBXW8 among all F-box proteins is explained by its unique F-box-independent binding mode. In CRL7, the RBX1 (also known as ROC1) RING domain is constrained in an orientation incompatible with binding E2~NEDD8 or E2~ubiquitin intermediates. Accordingly, purified recombinant CRL7 lacks auto-neddylation and ubiquitination activities. Instead, our data indicate that CRL7 serves as a substrate receptor linked via SKP1-FBXW8 to a neddylated CUL1-RBX1 catalytic module mediating ubiquitination. The structure reveals a distinctive CRL-CRL partnership, and provides a framework for understanding CUL7 assemblies safeguarding human health.
History
DepositionMar 17, 2022-
Header (metadata) releaseAug 24, 2022-
Map releaseAug 24, 2022-
UpdateOct 5, 2022-
Current statusOct 5, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14558.png

Downloads & links

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Map

FileDownload / File: emd_14558.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.89 Å/pix.
x 192 pix.
= 361.92 Å		1.89 Å/pix.
x 192 pix.
= 361.92 Å		1.89 Å/pix.
x 192 pix.
= 361.92 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.885 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.037
Minimum - Maximum-0.036283594 - 0.097893044
Average (Standard dev.)0.00011348178 (±0.00384765)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 361.91998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_14558_msk_1.map
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Half map: #2

Fileemd_14558_half_map_1.map
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Half map: #1

Fileemd_14558_half_map_2.map
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Sample components

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Entire : Structure of the CUL7-RBX1-FBXW8-SKP1-CUL1 N-terminal region form...

EntireName: Structure of the CUL7-RBX1-FBXW8-SKP1-CUL1 N-terminal region forming multi cullin-RING ligase complex
Components
  • Complex: Structure of the CUL7-RBX1-FBXW8-SKP1-CUL1 N-terminal region forming multi cullin-RING ligase complex

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Supramolecule #1: Structure of the CUL7-RBX1-FBXW8-SKP1-CUL1 N-terminal region form...

SupramoleculeName: Structure of the CUL7-RBX1-FBXW8-SKP1-CUL1 N-terminal region forming multi cullin-RING ligase complex
type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: 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

Concentration1.3 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.3000000000000003 µm / Nominal defocus min: 1.2 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 58.56 e/Å2

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 363067
FSC plot (resolution estimation)

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