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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: bioRxiv / Year: 2024
Title: Distinct Perception Mechanisms of BACH1 Quaternary Structure Degrons by Two F-box Proteins under Oxidative Stress.
Authors: Shiyun Cao / Huigang Shi / Sheena Faye Garcia / Yuki Kito / Hui Shi / Hailey V Goldberg / Jackeline Ponce / Beatrix Ueberheide / Luca Lignitto / Michele Pagano / Ning Zheng /
Abstract: The transcription factor BACH1 regulates heme homeostasis and oxidative stress responses and promotes cancer metastasis upon aberrant accumulation. Its stability is controlled by two F-box protein ...The transcription factor BACH1 regulates heme homeostasis and oxidative stress responses and promotes cancer metastasis upon aberrant accumulation. Its stability is controlled by two F-box protein ubiquitin ligases, FBXO22 and FBXL17. Here we show that the homodimeric BTB domain of BACH1 functions as a previously undescribed quaternary structure degron, which is deciphered by the two F-box proteins via distinct mechanisms. After BACH1 is released from chromatin by heme, FBXO22 asymmetrically recognizes a cross-protomer interface of the intact BACH1 BTB dimer, which is otherwise masked by the co-repressor NCOR1. If the BACH1 BTB dimer escapes the surveillance by FBXO22 due to oxidative modifications, its quaternary structure integrity is probed by a pair of FBXL17, which simultaneously engage and remodel the two BTB protomers into E3-bound monomers for ubiquitination. By unveiling the multifaceted regulatory mechanisms of BACH1 stability, our studies highlight the abilities of ubiquitin ligases to decode high-order protein assemblies and reveal therapeutic opportunities to block cancer invasion via compound-induced BACH1 destabilization.
History
DepositionSep 25, 2023-
Header (metadata) releaseNov 6, 2024-
Map releaseNov 6, 2024-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing 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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