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- EMDB-19766: Cryo-EM structure of SKP1-FBXO22 in complex with a BACH1 BTB dime... -

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Basic information

Entry
Database: EMDB / ID: EMD-19766
TitleCryo-EM structure of SKP1-FBXO22 in complex with a BACH1 BTB dimer at 3.2A resolution
Map data
Sample
  • Complex: SKP1-FBXO22-BACH1BTB complex
    • Complex: SKP1-FBXO22
      • Protein or peptide: F-box only protein 22
    • Complex: Transcription regulator protein BACH1
      • Protein or peptide: Transcription regulator protein BACH1
      • Protein or peptide: S-phase kinase-associated protein 1
KeywordsSKP1-FBXO22 E3 ligase SCF F-box protein BACH1 BTB / LIGASE
Function / homology
Function and homology information


regulation of skeletal muscle fiber development / Regulation of HMOX1 expression and activity / F-box domain binding / PcG protein complex / ligand-modulated transcription factor activity / 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 / regulation of metabolic process ...regulation of skeletal muscle fiber development / Regulation of HMOX1 expression and activity / F-box domain binding / PcG protein complex / ligand-modulated transcription factor activity / 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 / regulation of metabolic process / nucleocytoplasmic transport / SCF ubiquitin ligase complex / NFE2L2 regulating anti-oxidant/detoxification enzymes / 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 / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Heme signaling / Iron uptake and transport / 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 / DNA-binding transcription repressor activity, RNA polymerase II-specific / CLEC7A (Dectin-1) signaling / Z disc / SCF(Skp2)-mediated degradation of p27/p21 / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / RNA polymerase II transcription regulator complex / FCERI mediated NF-kB activation / Interleukin-1 signaling / Orc1 removal from chromatin / protein polyubiquitination / ubiquitin-protein transferase activity / Regulation of RUNX2 expression and 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 / 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 / protein ubiquitination / chromatin remodeling / protein domain specific binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / DNA repair / heme binding / centrosome / 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 / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / 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 / 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
Similarity search - Domain/homology
Transcription regulator protein BACH1 / S-phase kinase-associated protein 1 / F-box only protein 22
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsKhoshouei M / Goretzki B
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of SKP1-FBXO22 in complex with a BACH1 BTB dimer at 3.2A resolution
Authors: Khoshouei M / Goretzki B
History
DepositionFeb 29, 2024-
Header (metadata) releaseDec 11, 2024-
Map releaseDec 11, 2024-
UpdateDec 11, 2024-
Current statusDec 11, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19766.png

Downloads & links

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Map

FileDownload / File: emd_19766.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 200 pix.
= 169. Å		0.85 Å/pix.
x 200 pix.
= 169. Å		0.85 Å/pix.
x 200 pix.
= 169. Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.845 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.441
Minimum - Maximum-5.273945 - 6.425545
Average (Standard dev.)0.000069854344 (±0.122242965)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 169.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_19766_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_19766_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : SKP1-FBXO22-BACH1BTB complex

EntireName: SKP1-FBXO22-BACH1BTB complex
Components
  • Complex: SKP1-FBXO22-BACH1BTB complex
    • Complex: SKP1-FBXO22
      • Protein or peptide: F-box only protein 22
    • Complex: Transcription regulator protein BACH1
      • Protein or peptide: Transcription regulator protein BACH1
      • Protein or peptide: S-phase kinase-associated protein 1

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Supramolecule #1: SKP1-FBXO22-BACH1BTB complex

SupramoleculeName: SKP1-FBXO22-BACH1BTB complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 62 kDa/nm

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Supramolecule #2: SKP1-FBXO22

SupramoleculeName: SKP1-FBXO22 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Transcription regulator protein BACH1

SupramoleculeName: Transcription regulator protein BACH1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Transcription regulator protein BACH1

MacromoleculeName: Transcription regulator protein BACH1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.186162 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
QSMSVFAYES SVHSTNVLLS LNDQRKKDVL CDVTIFVEGQ RFRAHRSVLA ACSSYFHSRI VGQADGELNI TLPEEVTVKG FEPLIQFAY TAKLILSKEN VDEVCKCVEF LSVHNIEESC FQFLKF

UniProtKB: Transcription regulator protein BACH1

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Macromolecule #2: S-phase kinase-associated protein 1

MacromoleculeName: S-phase kinase-associated protein 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.679965 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MPSIKLQSSD GEIFEVDVEI AKQSVTIKTM LEDLGMDDEG DDDPVPLPNV NAAILKKVIQ WCTHHKDDPP PPEDDENKEK RTDDIPVWD QEFLKVDQGT LFELILAANY LDIKGLLDVT CKTVANMIKG KTPEEIRKTF NIKNDFTEEE EAQVRKENQW C EEK

UniProtKB: S-phase kinase-associated protein 1

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Macromolecule #3: F-box only protein 22

MacromoleculeName: F-box only protein 22 / type: protein_or_peptide / ID: 3 / 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

Concentration20 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: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1715031
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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