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- EMDB-42105: Cryo-EM structure of dimeric SCF-FBXL17-BACH1BTB E3 ligase comple... -

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Entry
Database: EMDB / ID: EMD-42105
TitleCryo-EM structure of dimeric SCF-FBXL17-BACH1BTB E3 ligase complex close conformation
Map dataThe global EM map of dimeric SCF-FBXL17-BACH1-BTB via Non-uniform refinement in cryoSPARC.
Sample
  • Complex: The SCF-F-box protein with BACH1 BTB Domain, dimeric SCF-BFXL17-BACH1BTB
    • Protein or peptide: Transcription regulator protein BACH1
    • Protein or peptide: S-phase kinase-associated protein 1
    • Protein or peptide: F-box/LRR-repeat protein 17
    • Protein or peptide: Cullin-1
    • Protein or peptide: E3 ubiquitin-protein ligase RBX1, N-terminally processed
KeywordsSCF / FBXL17 / BACH1 / F-box protein / CUL1 / Cullin / E3 ligase / LIGASE
Function / homology
Function and homology information


Regulation of HMOX1 expression and activity / Parkin-FBXW7-Cul1 ubiquitin ligase complex / F-box domain binding / PcG protein complex / ligand-activated transcription factor activity / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / regulation of smoothened signaling pathway / cellular response to chemical stress ...Regulation of HMOX1 expression and activity / Parkin-FBXW7-Cul1 ubiquitin ligase complex / F-box domain binding / PcG protein complex / ligand-activated transcription factor activity / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / regulation of smoothened signaling pathway / cellular response to chemical stress / positive regulation of ubiquitin protein ligase activity / Cul7-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / maintenance of protein location in nucleus / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / positive regulation of protein autoubiquitination / protein neddylation / regulation of metabolic process / neural crest cell differentiation / NEDD8 ligase activity / Cul5-RING ubiquitin ligase complex / negative regulation of response to oxidative stress / ubiquitin-ubiquitin ligase activity / SCF ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / Cul4A-RING E3 ubiquitin ligase complex / NFE2L2 regulating anti-oxidant/detoxification enzymes / Cul4B-RING E3 ubiquitin ligase complex / negative regulation of type I interferon production / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / ubiquitin ligase complex scaffold activity / Cul3-RING ubiquitin ligase complex / protein quality control for misfolded or incompletely synthesized proteins / entrainment of circadian clock by photoperiod / Prolactin receptor signaling / protein monoubiquitination / cullin family protein binding / ubiquitin-like ligase-substrate adaptor activity / protein K48-linked ubiquitination / Nuclear events stimulated by ALK signaling in cancer / positive regulation of TORC1 signaling / post-translational protein modification / intrinsic apoptotic signaling pathway / regulation of cellular response to insulin stimulus / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / T cell activation / molecular function activator activity / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Vpu mediated degradation of CD4 / animal organ morphogenesis / cellular response to amino acid stimulus / Degradation of DVL / Dectin-1 mediated noncanonical NF-kB signaling / Iron uptake and transport / Recognition of DNA damage by PCNA-containing replication complex / Activation of NF-kappaB in B cells / Degradation of GLI1 by the proteasome / Negative regulation of NOTCH4 signaling / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Vif-mediated degradation of APOBEC3G / Hedgehog 'on' state / Heme signaling / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / DNA Damage Recognition in GG-NER / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / RING-type E3 ubiquitin transferase / negative regulation of canonical Wnt signaling pathway / Degradation of beta-catenin by the destruction complex / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Dual Incision in GG-NER / Evasion by RSV of host interferon responses / NOTCH1 Intracellular Domain Regulates Transcription / CLEC7A (Dectin-1) signaling / DNA-binding transcription repressor activity, RNA polymerase II-specific / SCF(Skp2)-mediated degradation of p27/p21 / beta-catenin binding / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Regulation of expression of SLITs and ROBOs / Formation of Incision Complex in GG-NER / FCERI mediated NF-kB activation / Interleukin-1 signaling / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Orc1 removal from chromatin / protein polyubiquitination / RNA polymerase II transcription regulator complex / Regulation of RAS by GAPs / G1/S transition of mitotic cell cycle / positive regulation of protein catabolic process / cellular response to UV / Regulation of RUNX2 expression and activity / Cyclin D associated events in G1 / Regulation of PLK1 Activity at G2/M Transition / MAPK cascade
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. / SKP1 component, dimerisation ...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. / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / F-box-like domain superfamily / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / F-box-like / F-box domain / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / Cullin protein neddylation domain / : / Cullin, conserved site / Cullin family signature. / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation domain / Leucine Rich repeat / Basic-leucine zipper (bZIP) domain signature. / Cullin / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin family / Cullin family profile. / Basic-leucine zipper domain / Basic-leucine zipper domain superfamily / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily / Leucine-rich repeat / Zinc finger RING-type profile. / Leucine-rich repeat domain superfamily / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Transcription regulator protein BACH1 / E3 ubiquitin-protein ligase RBX1 / S-phase kinase-associated protein 1 / Cullin-1 / F-box/LRR-repeat protein 17
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.6 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_42105.png

Downloads & links

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Map

FileDownload / File: emd_42105.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe global EM map of dimeric SCF-FBXL17-BACH1-BTB via Non-uniform refinement in cryoSPARC.
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)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.743 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0261
Minimum - Maximum-0.084999934 - 0.2552071
Average (Standard dev.)-0.00031009794 (±0.0062373127)
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_42105_msk_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: The half map of dimeric SCF-FBXL17-BACH1-BTB via Non-uniform...

Fileemd_42105_half_map_1.map
AnnotationThe half map of dimeric SCF-FBXL17-BACH1-BTB via Non-uniform 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-BACH1-BTB via Non-uniform...

Fileemd_42105_half_map_2.map
AnnotationThe half map of dimeric SCF-FBXL17-BACH1-BTB via Non-uniform 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 SCF-F-box protein with BACH1 BTB Domain, dimeric SCF-BFXL17-B...

EntireName: The SCF-F-box protein with BACH1 BTB Domain, dimeric SCF-BFXL17-BACH1BTB
Components
  • Complex: The SCF-F-box protein with BACH1 BTB Domain, dimeric SCF-BFXL17-BACH1BTB
    • Protein or peptide: Transcription regulator protein BACH1
    • Protein or peptide: S-phase kinase-associated protein 1
    • Protein or peptide: F-box/LRR-repeat protein 17
    • Protein or peptide: Cullin-1
    • Protein or peptide: E3 ubiquitin-protein ligase RBX1, N-terminally processed

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Supramolecule #1: The SCF-F-box protein with BACH1 BTB Domain, dimeric SCF-BFXL17-B...

SupramoleculeName: The SCF-F-box protein with BACH1 BTB Domain, dimeric SCF-BFXL17-BACH1BTB
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #5, #3-#4, #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Cullin-1

MacromoleculeName: Cullin-1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 88.501945 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: KQIGLDQIWD DLRAGIQQVY TRQSMAKSRY MELYTHVYNY CTSVHQSNQA RGAGVPPSKS KKGQTPGGAQ FVGLELYKRL KEFLKNYLT NLLKDGEDLM DESVLKFYTQ QWEDYRFSSK VLNGICAYLN RHWVRRECDE GRKGIYEIYS LALVTWRDCL F RPLNKQVT ...String:
KQIGLDQIWD DLRAGIQQVY TRQSMAKSRY MELYTHVYNY CTSVHQSNQA RGAGVPPSKS KKGQTPGGAQ FVGLELYKRL KEFLKNYLT NLLKDGEDLM DESVLKFYTQ QWEDYRFSSK VLNGICAYLN RHWVRRECDE GRKGIYEIYS LALVTWRDCL F RPLNKQVT NAVLKLIEKE RNGETINTRL ISGVVQSYVE LGLNEDDAFA KGPTLTVYKE SFESQFLADT ERFYTRESTE FL QQNPVTE YMKKAEARLL EEQRRVQVYL HESTQDELAR KCEQVLIEKH LEIFHTEFQN LLDADKNEDL GRMYNLVSRI QDG LGELKK LLETHIHNQG LAAIEKCGEA ALNDPKMYVQ TVLDVHKKYN ALVMSAFNND AGFVAALDKA CGRFINNNAV TKMA QSSSK SPELLARYCD SLLKKSSKNP EEAELEDTLN QVMVVFKYIE DKDVFQKFYA KMLAKRLVHQ NSASDDAEAS MISKL KQAC GFEYTSKLQR MFQDIGVSKD LNEQFKKHLT NSEPLDLDFS IQVLSSGSWP FQQSCTFALP SELERSYQRF TAFYAS RHS GRKLTWLYQL SKGELVTNCF KNRYTLQAST FQMAILLQYN TEDAYTVQQL TDSTQIKMDI LAQVLQILLK SKLLVLE DE NANVDEVELK PDTLIKLYLG YKNKKLRVNI NVPMKTEQKQ EQETTHKNIE EDRKLLIQAA IVRIMKMRKV LKHQQLLG E VLTQLSSRFK PRVPVIKKCI DILIEKEYLE RVDGEKDTYS YLA

UniProtKB: Cullin-1

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Macromolecule #2: E3 ubiquitin-protein ligase RBX1, N-terminally processed

MacromoleculeName: E3 ubiquitin-protein ligase RBX1, N-terminally processed
type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.84041 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
GAGKKRFEVK KWNAVALWAW DIVVDNCAIC RNHIMDLCIE CQANQASATS EECTVAWGVC NHAFHFHCIS RWLKTRQVCP LDNREWEFQ KYGH

UniProtKB: E3 ubiquitin-protein ligase RBX1

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Macromolecule #3: S-phase kinase-associated protein 1

MacromoleculeName: S-phase kinase-associated protein 1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.580834 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MPSIKLQSSD GEIFEVDVEI AKQSTIKTML EDLGMDDEGD DDPVPLPNVN AAILKKVIQW CTHHKDDPPP PEDDENKEKR TDDIPVWDQ EFLKVDQGTL FELILAANYL DIKGLLDVTC KTVANMIKGK TPEEIRKTFN IKNDFTEEEE AQVRKENQWC E EK

UniProtKB: S-phase kinase-associated protein 1

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Macromolecule #4: F-box/LRR-repeat protein 17

MacromoleculeName: F-box/LRR-repeat protein 17 / type: protein_or_peptide / ID: 4 / 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 #5: Transcription regulator protein BACH1

MacromoleculeName: Transcription regulator protein BACH1 / type: protein_or_peptide / ID: 5 / 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
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 reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 4.6 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 model
PDB IDChain

6wcq

source_name: PDB, initial_model_type: experimental model

1ldj

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8ubu:
Cryo-EM structure of dimeric SCF-FBXL17-BACH1BTB E3 ligase complex close conformation

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