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- EMDB-42106: Cryo-EM structure of dimeric FBXL17-BACH1BTB E3 ubiquitin ligase ... -

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Basic information

Entry
Database: EMDB / ID: EMD-42106
TitleCryo-EM structure of dimeric FBXL17-BACH1BTB E3 ubiquitin ligase complex
Map dataThe local refinement EM map of dimeric SCF-FBXL17-BACH1BTB with a mask including the density of FBXL17-BACH1BTB via local refinement in cryoSPARC.
Sample
  • Complex: The structure of dimeric BFXL17-BACH1BTB
    • Protein or peptide: F-box/LRR-repeat protein 17
    • Protein or peptide: Transcription regulator protein BACH1
KeywordsFBXL17 / BACH1 / F-box protein / Cullin / E3 ligase / LIGASE
Function / homology
Function and homology information


Regulation of HMOX1 expression and activity / ligand-modulated transcription factor activity / regulation of smoothened signaling pathway / regulation of metabolic process / neural crest cell differentiation / SCF ubiquitin ligase complex / NFE2L2 regulating anti-oxidant/detoxification enzymes / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / protein quality control for misfolded or incompletely synthesized proteins / Regulation of BACH1 activity ...Regulation of HMOX1 expression and activity / ligand-modulated transcription factor activity / regulation of smoothened signaling pathway / regulation of metabolic process / neural crest cell differentiation / SCF ubiquitin ligase complex / NFE2L2 regulating anti-oxidant/detoxification enzymes / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / protein quality control for misfolded or incompletely synthesized proteins / Regulation of BACH1 activity / Heme signaling / DNA-binding transcription repressor activity, RNA polymerase II-specific / RNA polymerase II transcription regulator complex / protein polyubiquitination / nervous system development / DNA-binding transcription activator activity, RNA polymerase II-specific / proteasome-mediated ubiquitin-dependent protein catabolic process / DNA-binding transcription factor activity, RNA polymerase II-specific / protein ubiquitination / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / DNA repair / heme binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
: / BACH, basic leucine zipper (bZIP) domain / Basic leucine zipper domain, Maf-type / bZIP Maf transcription factor / Transcription factor, Skn-1-like, DNA-binding domain superfamily / : / Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / A Receptor for Ubiquitination Targets / F-box domain profile. ...: / BACH, basic leucine zipper (bZIP) domain / Basic leucine zipper domain, Maf-type / bZIP Maf transcription factor / Transcription factor, Skn-1-like, DNA-binding domain superfamily / : / Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / A Receptor for Ubiquitination Targets / F-box domain profile. / F-box-like domain superfamily / F-box-like / F-box domain / Basic-leucine zipper (bZIP) domain signature. / Leucine Rich repeat / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain / Basic-leucine zipper domain superfamily / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily
Similarity search - Domain/homology
Transcription regulator protein BACH1 / F-box/LRR-repeat protein 17
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 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_42106.png

Downloads & links

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Map

FileDownload / File: emd_42106.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe local refinement EM map of dimeric SCF-FBXL17-BACH1BTB with a mask including the density of FBXL17-BACH1BTB via local refinement in cryoSPARC.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.74 Å/pix.
x 480 pix.
= 356.64 Å		0.74 Å/pix.
x 480 pix.
= 356.64 Å		0.74 Å/pix.
x 480 pix.
= 356.64 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: 0.08
Minimum - Maximum-0.41929874 - 0.7758919
Average (Standard dev.)-0.000617933 (±0.008254493)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 356.63998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_42106_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 with a...

Fileemd_42106_half_map_1.map
AnnotationThe half map of dimeric SCF-FBXL17-BACH1BTB with a mask including the density of FBXL17-BACH1BTB via local refinement in cryoSPARC.
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 with a...

Fileemd_42106_half_map_2.map
AnnotationThe half map of dimeric SCF-FBXL17-BACH1BTB with a mask including the density of FBXL17-BACH1BTB via local refinement in cryoSPARC.
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 BFXL17-BACH1BTB

EntireName: The structure of dimeric BFXL17-BACH1BTB
Components
  • Complex: The structure of dimeric BFXL17-BACH1BTB
    • Protein or peptide: F-box/LRR-repeat protein 17
    • Protein or peptide: Transcription regulator protein BACH1

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Supramolecule #1: The structure of dimeric BFXL17-BACH1BTB

SupramoleculeName: The structure of dimeric BFXL17-BACH1BTB / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: F-box/LRR-repeat protein 17

MacromoleculeName: F-box/LRR-repeat protein 17 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.505512 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: CHREPPPETP DINQLPPSIL LKIFSNLSLD ERCLSASLVC KYWRDLCLDF QFWKQLDLSS RQQVTDELLE KIASRSQNII EINISDCRS MSDNGVCVLA FKCPGLLRYT AYRCKQLSDT SIIAVASHCP LLQKVHVGNQ DKLTDEGLKQ LGSKCRELKD I HFGQCYKI ...String:
CHREPPPETP DINQLPPSIL LKIFSNLSLD ERCLSASLVC KYWRDLCLDF QFWKQLDLSS RQQVTDELLE KIASRSQNII EINISDCRS MSDNGVCVLA FKCPGLLRYT AYRCKQLSDT SIIAVASHCP LLQKVHVGNQ DKLTDEGLKQ LGSKCRELKD I HFGQCYKI SDEGMIVIAK GCLKLQRIYM QENKLVTDQS VKAFAEHCPE LQYVGFMGCS VTSKGVIHLT KLRNLSSLDL RH ITELDNE TVMEIVKRCK NLSSLNLCLN WIINDRCVEV IAKEGQNLKE LYLVSCKITD YALIAIGRYS MTIETVDVGW CKE ITDQGA TLIAQSSKSL RYLGLMRCDK VNEVTVEQLV QQYPHITFST VLQDCKRTLE RAYQMGWTPN MSAASS

UniProtKB: F-box/LRR-repeat protein 17

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Macromolecule #2: Transcription regulator protein BACH1

MacromoleculeName: Transcription regulator protein BACH1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.839761 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
SVFAYESSVH STNVLLSLND QRKKDVLCDV TIFVEGQRFR AHRSVLAACS SYFHSRIVGQ ADGELNITLP EEVTVKGFEP LIQFAYTAK LILSKENVDE VCKCVEFLSV HNIEESCFQF LKF

UniProtKB: Transcription regulator protein BACH1

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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

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 reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 71155
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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Atomic model buiding 1

Initial modelPDB ID:

6wcq


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8ubv:
Cryo-EM structure of dimeric FBXL17-BACH1BTB E3 ubiquitin ligase complex

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