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- EMDB-19768: Cryo-EM structure of SKP1-FBXO22 -

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Basic information

Entry
Database: EMDB / ID: EMD-19768
TitleCryo-EM structure of SKP1-FBXO22
Map data
Sample
  • Complex: SKP1-FBXO22 complex
    • Protein or peptide: S-phase kinase-associated protein 1
    • Protein or peptide: F-box only protein 22
KeywordsSKP1-FBXO22 E3 ligase SCF F-box protein / LIGASE
Function / homology
Function and homology information


regulation of skeletal muscle fiber development / F-box domain binding / PcG protein complex / positive regulation of ubiquitin protein ligase activity / Cul7-RING ubiquitin ligase complex / maintenance of protein location in nucleus / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / nucleocytoplasmic transport / SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process ...regulation of skeletal muscle fiber development / F-box domain binding / PcG protein complex / positive regulation of ubiquitin protein ligase activity / Cul7-RING ubiquitin ligase complex / maintenance of protein location in nucleus / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / nucleocytoplasmic transport / SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / ubiquitin ligase complex scaffold activity / Prolactin receptor signaling / cullin family protein binding / protein monoubiquitination / ubiquitin-like ligase-substrate adaptor activity / protein K48-linked ubiquitination / Nuclear events stimulated by ALK signaling in cancer / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / molecular function activator activity / cellular response to starvation / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Vpu mediated degradation of CD4 / Dectin-1 mediated noncanonical NF-kB signaling / Activation of NF-kappaB in B cells / Degradation of GLI1 by the proteasome / Iron uptake and transport / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Negative regulation of NOTCH4 signaling / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / protein modification process / beta-catenin binding / Degradation of beta-catenin by the destruction complex / NOTCH1 Intracellular Domain Regulates Transcription / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / FCERI mediated NF-kB activation / Z disc / Interleukin-1 signaling / Orc1 removal from chromatin / protein polyubiquitination / Regulation of RUNX2 expression and activity / ubiquitin-protein transferase activity / Cyclin D associated events in G1 / : / Regulation of PLK1 Activity at G2/M Transition / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Neddylation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / chromatin remodeling / protein domain specific binding / centrosome / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
FIST, C-domain / FIST C domain / FIST_C / F-box domain / 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 ...FIST, C-domain / FIST C domain / FIST_C / F-box domain / 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 / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / SKP1/BTB/POZ domain superfamily
Similarity search - Domain/homology
S-phase kinase-associated protein 1 / F-box only protein 22
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsKhoshouei M
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell / Year: 2024
Title: Dual BACH1 regulation by complementary SCF-type E3 ligases.
Authors: Benedikt Goretzki / Maryam Khoshouei / Martin Schröder / Patrick Penner / Luca Egger / Christine Stephan / Dayana Argoti / Nele Dierlamm / Jimena Maria Rada / Sandra Kapps / Catrin Swantje ...Authors: Benedikt Goretzki / Maryam Khoshouei / Martin Schröder / Patrick Penner / Luca Egger / Christine Stephan / Dayana Argoti / Nele Dierlamm / Jimena Maria Rada / Sandra Kapps / Catrin Swantje Müller / Zacharias Thiel / Merve Mutlu / Claude Tschopp / David Furkert / Felix Freuler / Simon Haenni / Laurent Tenaillon / Britta Knapp / Alexandra Hinniger / Philipp Hoppe / Enrico Schmidt / Sascha Gutmann / Mario Iurlaro / Grigory Ryzhakov / César Fernández /
Abstract: Broad-complex, tramtrack, and bric-à-brac domain (BTB) and CNC homolog 1 (BACH1) is a key regulator of the cellular oxidative stress response and an oncogene that undergoes tight post-translational ...Broad-complex, tramtrack, and bric-à-brac domain (BTB) and CNC homolog 1 (BACH1) is a key regulator of the cellular oxidative stress response and an oncogene that undergoes tight post-translational control by two distinct F-box ubiquitin ligases, SCF and SCF. However, how both ligases recognize BACH1 under oxidative stress is unclear. In our study, we elucidate the mechanism by which FBXO22 recognizes a quaternary degron in a domain-swapped β-sheet of the BACH1 BTB dimer. Cancer-associated mutations and cysteine modifications destabilize the degron and impair FBXO22 binding but simultaneously expose an otherwise shielded degron in the dimer interface, allowing FBXL17 to recognize BACH1 as a monomer. These findings shed light on a ligase switch mechanism that enables post-translational regulation of BACH1 by complementary ligases depending on the stability of its BTB domain. Our results provide mechanistic insights into the oxidative stress response and may spur therapeutic approaches for targeting oxidative stress-related disorders and cancer.
History
DepositionFeb 29, 2024-
Header (metadata) releaseDec 11, 2024-
Map releaseDec 11, 2024-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19768.png

Downloads & links

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Map

FileDownload / File: emd_19768.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
0.66 Å/pix.
x 240 pix.
= 158.4 Å		0.66 Å/pix.
x 240 pix.
= 158.4 Å		0.66 Å/pix.
x 240 pix.
= 158.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.66 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.19
Minimum - Maximum-1.2017814 - 1.3987207
Average (Standard dev.)0.00015785785 (±0.03810355)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 158.40001 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19768_msk_1.map
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Additional map: #1

Fileemd_19768_additional_1.map
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Half map: #1

Fileemd_19768_half_map_1.map
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Half map: #2

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Sample components

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Entire : SKP1-FBXO22 complex

EntireName: SKP1-FBXO22 complex
Components
  • Complex: SKP1-FBXO22 complex
    • Protein or peptide: S-phase kinase-associated protein 1
    • Protein or peptide: F-box only protein 22

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Supramolecule #1: SKP1-FBXO22 complex

SupramoleculeName: SKP1-FBXO22 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 62 kDa/nm

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

MacromoleculeName: S-phase kinase-associated protein 1 / type: protein_or_peptide / ID: 1 / Details: S-phase kinase-associated protein 1 (SKP1) / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.54877 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
PSIKLQSSDG EIFEVDVEIA KQSVTIKTML 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 #2: F-box only protein 22

MacromoleculeName: F-box only protein 22 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 43.597062 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GGSGSSVDPR STFVLSNLAE VVERVLTFLP AKALLRVACV CRLWRECVRR VLRTHRSVTW ISAGLAEAGH LEGHCLVRVV AEELENVRI LPHTVLYMAD SETFISLEEC RGHKRARKRT SMETALALEK LFPKQCQVLG IVTPGIVVTP MGSGSNRPQE I EIGESGFA ...String:
GGSGSSVDPR STFVLSNLAE VVERVLTFLP AKALLRVACV CRLWRECVRR VLRTHRSVTW ISAGLAEAGH LEGHCLVRVV AEELENVRI LPHTVLYMAD SETFISLEEC RGHKRARKRT SMETALALEK LFPKQCQVLG IVTPGIVVTP MGSGSNRPQE I EIGESGFA LLFPQIEGIK IQPFHFIKDP KNLTLERHQL TEVGLLDNPE LRVVLVFGYN CCKVGASNYL QQVVSTFSDM NI ILAGGQV DNLSSLTSEK NPLDIDASGV VGLSFSGHRI QSATVLLNED VSDEKTAEAA MQRLKAANIP EHNTIGFMFA CVG RGFQYY RAKGNVEADA FRKFFPSVPL FGFFGNGEIG CDRIVTGNFI LRKCNEVKDD DLFHSYTTIM ALIHLGSSK

UniProtKB: F-box only protein 22

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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

Concentration16 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Details: THERMO SCIENTIFIC FALCON 4i (4k x 4k) direct detector
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 717992
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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