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- EMDB-34463: Cryo-EM Structure of the KBTBD2-CRL3~N8(removed)-CSN(no CSN3/8) c... -

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Basic information

Entry
Database: EMDB / ID: EMD-34463
TitleCryo-EM Structure of the KBTBD2-CRL3~N8(removed)-CSN(no CSN3/8) complex
Map data
Sample
  • Complex: Cryo-EM Structure of the KBTBD2-CRL3~N8-CSN(no CSN3/8) complex
    • Complex: CSN
    • Complex: KBTBD2,CRL3
    • Complex: N8
Keywordsligase / complex
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.15 Å
AuthorsHu Y / Mao Q / Chen Z / Sun L
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81900729 China
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: Dynamic molecular architecture and substrate recruitment of cullin3-RING E3 ligase CRL3.
Authors: Yuxia Hu / Zhao Zhang / Qiyu Mao / Xiang Zhang / Aihua Hao / Yu Xun / Yeda Wang / Lin Han / Wuqiang Zhan / Qianying Liu / Yue Yin / Chao Peng / Eva Marie Y Moresco / Zhenguo Chen / Bruce Beutler / Lei Sun /
Abstract: Phosphatidylinositol 3-kinase α, a heterodimer of catalytic p110α and one of five regulatory subunits, mediates insulin- and insulin like growth factor-signaling and, frequently, oncogenesis. ...Phosphatidylinositol 3-kinase α, a heterodimer of catalytic p110α and one of five regulatory subunits, mediates insulin- and insulin like growth factor-signaling and, frequently, oncogenesis. Cellular levels of the regulatory p85α subunit are tightly controlled by regulated proteasomal degradation. In adipose tissue and growth plates, failure of K48-linked p85α ubiquitination causes diabetes, lipodystrophy and dwarfism in mice, as in humans with SHORT syndrome. Here we elucidated the structures of the key ubiquitin ligase complexes regulating p85α availability. Specificity is provided by the substrate receptor KBTBD2, which recruits p85α to the cullin3-RING E3 ubiquitin ligase (CRL3). CRL3 forms multimers, which disassemble into dimers upon substrate binding (CRL3-p85α) and/or neddylation by the activator NEDD8 (CRL3~N8), leading to p85α ubiquitination and degradation. Deactivation involves dissociation of NEDD8 mediated by the COP9 signalosome and displacement of KBTBD2 by the inhibitor CAND1. The hereby identified structural basis of p85α regulation opens the way to better understanding disturbances of glucose regulation, growth and cancer.
History
DepositionOct 8, 2022-
Header (metadata) releaseOct 11, 2023-
Map releaseOct 11, 2023-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34463.png

Downloads & links

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Map

FileDownload / File: emd_34463.map.gz / Format: CCP4 / Size: 38.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
2.09 Å/pix.
x 216 pix.
= 451.008 Å		2.09 Å/pix.
x 216 pix.
= 451.008 Å		2.09 Å/pix.
x 216 pix.
= 451.008 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 2.088 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.001
Minimum - Maximum-0.0006329404 - 1.7903123
Average (Standard dev.)0.002591077 (±0.032012288)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions216216216
Spacing216216216
CellA=B=C: 451.00803 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_34463_half_map_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_34463_half_map_2.map
Projections & Slices
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Sample components

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Entire : Cryo-EM Structure of the KBTBD2-CRL3~N8-CSN(no CSN3/8) complex

EntireName: Cryo-EM Structure of the KBTBD2-CRL3~N8-CSN(no CSN3/8) complex
Components
  • Complex: Cryo-EM Structure of the KBTBD2-CRL3~N8-CSN(no CSN3/8) complex
    • Complex: CSN
    • Complex: KBTBD2,CRL3
    • Complex: N8

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Supramolecule #1: Cryo-EM Structure of the KBTBD2-CRL3~N8-CSN(no CSN3/8) complex

SupramoleculeName: Cryo-EM Structure of the KBTBD2-CRL3~N8-CSN(no CSN3/8) complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#11
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: CSN

SupramoleculeName: CSN / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#8

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Supramolecule #3: KBTBD2,CRL3

SupramoleculeName: KBTBD2,CRL3 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #9-#11

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Supramolecule #4: N8

SupramoleculeName: N8 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #12

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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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 53.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4d10


Details: 6r7f
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 7.15 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 63653
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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