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- PDB-8s7d: Cryo-EM structure of SKP1-FBXO22 in complex with a BACH1 BTB dime... -

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Basic information

Entry
Database: PDB / ID: 8s7d
TitleCryo-EM structure of SKP1-FBXO22 in complex with a BACH1 BTB dimer at 3.2A resolution
Components
  • F-box only protein 22
  • S-phase kinase-associated protein 1
  • Transcription regulator protein BACH1
KeywordsLIGASE / SKP1-FBXO22 E3 ligase SCF F-box protein BACH1 BTB
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsKhoshouei, M. / Goretzki, B.
Funding support1items
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, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription regulator protein BACH1
B: Transcription regulator protein BACH1
C: S-phase kinase-associated protein 1
D: F-box only protein 22


Theoretical massNumber of molelcules
Total (without water)90,6494
Polymers90,6494
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Transcription regulator protein BACH1 / BTB and CNC homolog 1 / HA2303


Mass: 14186.162 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BACH1 / Production host: Escherichia coli (E. coli) / References: UniProt: O14867
#2: Protein S-phase kinase-associated protein 1 / Cyclin-A/CDK2-associated protein p19 / p19A / Organ of Corti protein 2 / OCP-2 / Organ of Corti ...Cyclin-A/CDK2-associated protein p19 / p19A / Organ of Corti protein 2 / OCP-2 / Organ of Corti protein II / OCP-II / RNA polymerase II elongation factor-like protein / SIII / Transcription elongation factor B polypeptide 1-like / p19skp1


Mass: 18679.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SKP1, EMC19, OCP2, SKP1A, TCEB1L / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P63208
#3: Protein F-box only protein 22 / F-box protein FBX22p44


Mass: 43597.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FBXO22, FBX22 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8NEZ5
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1SKP1-FBXO22-BACH1BTB complexCOMPLEXall0MULTIPLE SOURCES
2SKP1-FBXO22COMPLEX#31RECOMBINANT
3Transcription regulator protein BACH1COMPLEX#1-#21RECOMBINANT
Molecular weightValue: 62 kDa/nm / Experimental value: YES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
33Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Spodoptera frugiperda (fall armyworm)7108
33Escherichia coli (E. coli)562
Buffer solutionpH: 7.5
SpecimenConc.: 20 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)
Details: THERMO SCIENTIFIC FALCON 4i (4k x 4k) direct detector

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1715031 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0025581
ELECTRON MICROSCOPYf_angle_d0.5527536
ELECTRON MICROSCOPYf_dihedral_angle_d3.807726
ELECTRON MICROSCOPYf_chiral_restr0.042882
ELECTRON MICROSCOPYf_plane_restr0.004957

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