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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 / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / 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 / 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 / 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 / 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: To Be Published
Title: Cryo-EM structure of SKP1-FBXO22 at 3.4A resolution
Authors: Khoshouei M
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_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

Image control

Size
Brightness
Contrast
Others
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
Density

Histogram

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

Fileemd_19768_half_map_2.map
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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

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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