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- EMDB-42115: Cryo-EM structure of dimeric SCF-FBXL17-BACH1BTB open conformation -

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Basic information

Entry
Database: EMDB / ID: EMD-42115
TitleCryo-EM structure of dimeric SCF-FBXL17-BACH1BTB open conformation
Map dataThe overall EM map of dimeric SCF-FBXL17-BACH1BTB open conformation generated from Non-uniform refinement with C2 symmetry imposed.
Sample
  • Complex: The structure of dimeric FBXL17-BACH1BTB open conformation
KeywordsFBXL17 / BACH1 / F-box protein / Cullin / E3 ligase / LIGASE
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.6 Å
AuthorsShi H / Cao S / Zheng N
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Cell / Year: 2024
Title: Recognition of BACH1 quaternary structure degrons by two F-box proteins under oxidative stress.
Authors: Shiyun Cao / Sheena Faye Garcia / Huigang Shi / Ellie I James / Yuki Kito / Hui Shi / Haibin Mao / Sharon Kaisari / Gergely Rona / Sophia Deng / Hailey V Goldberg / Jackeline Ponce / Beatrix ...Authors: Shiyun Cao / Sheena Faye Garcia / Huigang Shi / Ellie I James / Yuki Kito / Hui Shi / Haibin Mao / Sharon Kaisari / Gergely Rona / Sophia Deng / Hailey V Goldberg / Jackeline Ponce / Beatrix Ueberheide / Luca Lignitto / Miklos Guttman / Michele Pagano / Ning Zheng /
Abstract: Ubiquitin-dependent proteolysis regulates diverse cellular functions with high substrate specificity, which hinges on the ability of ubiquitin E3 ligases to decode the targets' degradation signals, i. ...Ubiquitin-dependent proteolysis regulates diverse cellular functions with high substrate specificity, which hinges on the ability of ubiquitin E3 ligases to decode the targets' degradation signals, i.e., degrons. Here, we show that BACH1, a transcription repressor of antioxidant response genes, features two distinct unconventional degrons encrypted in the quaternary structure of its homodimeric BTB domain. These two degrons are both functionalized by oxidative stress and are deciphered by two complementary E3s. FBXO22 recognizes a degron constructed by the BACH1 BTB domain dimer interface, which is unmasked from transcriptional co-repressors after oxidative stress releases BACH1 from chromatin. When this degron is impaired by oxidation, a second BACH1 degron manifested by its destabilized BTB dimer is probed by a pair of FBXL17 proteins that remodels the substrate into E3-bound monomers for ubiquitination. Our findings highlight the multidimensionality of protein degradation signals and the functional complementarity of different ubiquitin ligases targeting the same substrate.
History
DepositionSep 25, 2023-
Header (metadata) releaseNov 6, 2024-
Map releaseNov 6, 2024-
UpdateJan 8, 2025-
Current statusJan 8, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42115.png

Downloads & links

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Map

FileDownload / File: emd_42115.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe overall EM map of dimeric SCF-FBXL17-BACH1BTB open conformation generated from Non-uniform refinement with C2 symmetry imposed.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.74 Å/pix.
x 512 pix.
= 380.416 Å		0.74 Å/pix.
x 512 pix.
= 380.416 Å		0.74 Å/pix.
x 512 pix.
= 380.416 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.743 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.022
Minimum - Maximum-0.13439932 - 0.27271882
Average (Standard dev.)-0.00030126696 (±0.006297993)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 380.416 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_42115_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: The half map of dimeric SCF-FBXL17-BACH1BTB open conformation...

Fileemd_42115_half_map_1.map
AnnotationThe half map of dimeric SCF-FBXL17-BACH1BTB open conformation generated from Non-uniform refinement with C2 symmetry imposed.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: The half map of dimeric SCF-FBXL17-BACH1BTB open conformation...

Fileemd_42115_half_map_2.map
AnnotationThe half map of dimeric SCF-FBXL17-BACH1BTB open conformation generated from Non-uniform refinement with C2 symmetry imposed.
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 structure of dimeric FBXL17-BACH1BTB open conformation

EntireName: The structure of dimeric FBXL17-BACH1BTB open conformation
Components
  • Complex: The structure of dimeric FBXL17-BACH1BTB open conformation

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Supramolecule #1: The structure of dimeric FBXL17-BACH1BTB open conformation

SupramoleculeName: The structure of dimeric FBXL17-BACH1BTB open conformation
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
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
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 25.0 µm / Nominal defocus min: 5.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: ab-initio reconstruction
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 5.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 59624
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC

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