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- EMDB-42049: Cryo-EM Structure of FBOX22-BACH1BTB -

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Basic information

Entry
Database: EMDB / ID: EMD-42049
TitleCryo-EM Structure of FBOX22-BACH1BTB
Map dataFocused refinement EM map of FBXO22-BACH1BTB
Sample
  • Complex: FBXO22-BACH1BTB
    • Protein or peptide: F-box only protein 22
    • Protein or peptide: Transcription regulator protein BACH1
KeywordsF-box protein / FBXO22 / BACH1 / LIGASE
Function / homology
Function and homology information


regulation of skeletal muscle fiber development / Regulation of HMOX1 expression and activity / ligand-modulated transcription factor activity / regulation of metabolic process / nucleocytoplasmic transport / NFE2L2 regulating anti-oxidant/detoxification enzymes / Regulation of BACH1 activity / cellular response to starvation / Heme signaling / protein modification process ...regulation of skeletal muscle fiber development / Regulation of HMOX1 expression and activity / ligand-modulated transcription factor activity / regulation of metabolic process / nucleocytoplasmic transport / NFE2L2 regulating anti-oxidant/detoxification enzymes / Regulation of BACH1 activity / cellular response to starvation / Heme signaling / protein modification process / DNA-binding transcription repressor activity, RNA polymerase II-specific / Z disc / RNA polymerase II transcription regulator complex / protein polyubiquitination / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Neddylation / DNA-binding transcription activator activity, RNA polymerase II-specific / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / DNA-binding transcription factor activity, RNA polymerase II-specific / 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
FIST, C-domain / FIST C domain / FIST_C / BACH, basic leucine zipper (bZIP) domain / F-box domain / Basic leucine zipper domain, Maf-type / bZIP Maf transcription factor / Transcription factor, Skn-1-like, DNA-binding domain superfamily / : / F-box-like domain superfamily ...FIST, C-domain / FIST C domain / FIST_C / BACH, basic leucine zipper (bZIP) domain / F-box domain / Basic leucine zipper domain, Maf-type / bZIP Maf transcription factor / Transcription factor, Skn-1-like, DNA-binding domain superfamily / : / F-box-like domain superfamily / F-box domain / Basic-leucine zipper (bZIP) domain signature. / 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
Similarity search - Domain/homology
Transcription regulator protein BACH1 / F-box only protein 22
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 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 20, 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_42049.png

Downloads & links

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Map

FileDownload / File: emd_42049.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFocused refinement EM map of FBXO22-BACH1BTB
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 400 pix.
= 336. Å		0.84 Å/pix.
x 400 pix.
= 336. Å		0.84 Å/pix.
x 400 pix.
= 336. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.593
Minimum - Maximum-3.4948754 - 4.0048046
Average (Standard dev.)-0.0014305247 (±0.048752166)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 336.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_42049_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map for local refinement in cryoSPARC

Fileemd_42049_half_map_1.map
AnnotationHalf map for local refinement in cryoSPARC
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map for local refinement in cryoSPARC

Fileemd_42049_half_map_2.map
AnnotationHalf map for 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 : FBXO22-BACH1BTB

EntireName: FBXO22-BACH1BTB
Components
  • Complex: FBXO22-BACH1BTB
    • Protein or peptide: F-box only protein 22
    • Protein or peptide: Transcription regulator protein BACH1

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Supramolecule #1: FBXO22-BACH1BTB

SupramoleculeName: FBXO22-BACH1BTB / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: F-box only protein 22

MacromoleculeName: F-box only protein 22 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.56227 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MEPVGCCGEC RGSSVDPRST FVLSNLAEVV ERVLTFLPAK ALLRVACVCR LWRECVRRVL RTHRSVTWIS AGLAEAGHLE GHCLVRVVA EELENVRILP HTVLYMADSE TFISLEECRG HKRARKRTSM ETALALEKLF PKQCQVLGIV TPGIVVTPMG S GSNRPQEI ...String:
MEPVGCCGEC RGSSVDPRST FVLSNLAEVV ERVLTFLPAK ALLRVACVCR LWRECVRRVL RTHRSVTWIS AGLAEAGHLE GHCLVRVVA EELENVRILP HTVLYMADSE TFISLEECRG HKRARKRTSM ETALALEKLF PKQCQVLGIV TPGIVVTPMG S GSNRPQEI EIGESGFALL FPQIEGIKIQ PFHFIKDPKN LTLERHQLTE VGLLDNPELR VVLVFGYNCC KVGASNYLQQ VV STFSDMN IILAGGQVDN LSSLTSEKNP LDIDASGVVG LSFSGHRIQS ATVLLNEDVS DEKTAEAAMQ RLKAANIPEH NTI GFMFAC VGRGFQYYRA KGNVEADAFR KFFPSVPLFG FFGNGEIGCD RIVTGNFILR KCNEVKDDDL FHSYTTIMAL IHLG SSK

UniProtKB: F-box only protein 22

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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 (E. coli)
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
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec.
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 59.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.8 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: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 171378
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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