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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-modulated transcription factor activity / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / positive regulation of ubiquitin protein ligase activity / Cul7-RING ubiquitin ligase complex ...Regulation of HMOX1 expression and activity / Parkin-FBXW7-Cul1 ubiquitin ligase complex / F-box domain binding / PcG protein complex / ligand-modulated transcription factor activity / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / 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 / cellular response to chemical stress / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / regulation of smoothened signaling pathway / positive regulation of protein autoubiquitination / RNA polymerase II transcription initiation surveillance / protein neddylation / NEDD8 ligase activity / VCB complex / negative regulation of response to oxidative stress / neural crest cell differentiation / regulation of metabolic process / Cul5-RING ubiquitin ligase complex / NFE2L2 regulating anti-oxidant/detoxification enzymes / SCF ubiquitin ligase complex / negative regulation of type I interferon production / ubiquitin-ubiquitin ligase activity / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Cul2-RING ubiquitin ligase complex / Cul3-RING ubiquitin ligase complex / Cul4A-RING E3 ubiquitin ligase complex / Cul4-RING E3 ubiquitin ligase complex / negative regulation of mitophagy / Prolactin receptor signaling / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / protein quality control for misfolded or incompletely synthesized proteins / cullin family protein binding / protein monoubiquitination / ubiquitin-like ligase-substrate adaptor activity / protein K48-linked ubiquitination / Nuclear events stimulated by ALK signaling in cancer / transcription-coupled nucleotide-excision repair / positive regulation of TORC1 signaling / regulation of cellular response to insulin stimulus / negative regulation of insulin receptor signaling pathway / intrinsic apoptotic signaling pathway / post-translational protein modification / molecular function activator activity / Regulation of BACH1 activity / T cell activation / MAP3K8 (TPL2)-dependent MAPK1/3 activation / animal organ morphogenesis / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Vpu mediated degradation of CD4 / cellular response to amino acid stimulus / Degradation of DVL / Dectin-1 mediated noncanonical NF-kB signaling / Activation of NF-kappaB in B cells / Degradation of GLI1 by the proteasome / Heme signaling / Iron uptake and transport / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Negative regulation of NOTCH4 signaling / G1/S transition of mitotic cell cycle / negative regulation of canonical Wnt signaling pathway / Recognition of DNA damage by PCNA-containing replication complex / Hedgehog 'on' state / Vif-mediated degradation of APOBEC3G / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / beta-catenin binding / Degradation of beta-catenin by the destruction complex / RING-type E3 ubiquitin transferase / DNA Damage Recognition in GG-NER / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / 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 / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / SCF(Skp2)-mediated degradation of p27/p21 / RNA polymerase II transcription regulator complex / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / FCERI mediated NF-kB activation / Formation of TC-NER Pre-Incision Complex / Regulation of expression of SLITs and ROBOs / Formation of Incision Complex in GG-NER / Interleukin-1 signaling / protein polyubiquitination / Orc1 removal from chromatin / Regulation of RAS by GAPs / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Regulation of RUNX2 expression and activity
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 / : / A Receptor for Ubiquitination Targets / Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / 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 / : / A Receptor for Ubiquitination Targets / Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / F-box domain profile. / F-box-like / F-box-like domain superfamily / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / 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 / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Leucine Rich repeat / Cullin / Basic-leucine zipper domain / Basic-leucine zipper domain superfamily / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin alpha solenoid domain / Cullin family profile. / 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 / Leucine-rich repeat domain superfamily / Zinc finger RING-type profile. / 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: 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_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)

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: 0.0261
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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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_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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