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- EMDB-62223: Cryo-EM structure of the SKP1-FBXO3 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-62223
TitleCryo-EM structure of the SKP1-FBXO3 complex
Map data
Sample
  • Complex: Cryo-EM of the CUL1-RBX1-SKP1-FBXO3 SCF ubiquition ligase complex
    • Protein or peptide: S-phase kinase-associated protein 1
    • Protein or peptide: F-box only protein 3
KeywordsCryo-EM / PROTEIN BINDING / LIGASE
Function / homology
Function and homology information


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 / SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / ubiquitin ligase complex scaffold activity / Prolactin receptor signaling ...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 / 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 / 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 / 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 / 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 / Neddylation / response to lipopolysaccharide / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / chromatin remodeling / protein domain specific binding / centrosome / proteolysis / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
: / ApaG domain / ApaG domain superfamily / ApaG domain / ApaG domain profile. / SMI1 / KNR4 family (SUKH-1) / Knr4/Smi1-like domain / SMI1 / KNR4 family / Knr4/Smi1-like domain superfamily / A Receptor for Ubiquitination Targets ...: / ApaG domain / ApaG domain superfamily / ApaG domain / ApaG domain profile. / SMI1 / KNR4 family (SUKH-1) / Knr4/Smi1-like domain / SMI1 / KNR4 family / Knr4/Smi1-like domain superfamily / A Receptor for Ubiquitination Targets / F-box domain profile. / F-box-like domain superfamily / F-box-like / 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 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.74 Å
AuthorsWei J / Xu C
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Proteins / Year: 2025
Title: Structural Insight Into the SKP1-CUL1-FBXO3-RBX1 Complex.
Authors: Jiajia Wei / Chao Xu /
Abstract: The cryo-EM structure of human SCF, which consists of CUL1, RBX1, SKP1 and FBXO3 was solved at a nominal resolution of 3.70 Å. Although a previous study reported the crystal structure of the FBXO3 ...The cryo-EM structure of human SCF, which consists of CUL1, RBX1, SKP1 and FBXO3 was solved at a nominal resolution of 3.70 Å. Although a previous study reported the crystal structure of the FBXO3 ApaG domain, how FBXO3 is incorporated into the SCF complex remains elusive. In the cryo-EM structure of SCF, the F-box domain of FBXO3 primarily associates with SKP1 via extensive hydrophobic interactions and interacts with the N-terminal region of CUL1 via hydrophobic interactions. The weak cryo-EM map of the RBX1 globular region is close to the FBXO3 ApaG domain, suggesting that unmodified SCF exhibits a closed conformation and that CUL1 neddylation is likely required to achieve high E3 activity. The structural study provides insight into the assembly of SCF and its activation mediated by CUL1 neddylation.
History
DepositionOct 30, 2024-
Header (metadata) releaseFeb 19, 2025-
Map releaseFeb 19, 2025-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62223.png

Downloads & links

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Map

FileDownload / File: emd_62223.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 384 pix.
= 314.88 Å		0.82 Å/pix.
x 384 pix.
= 314.88 Å		0.82 Å/pix.
x 384 pix.
= 314.88 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.9632491 - 1.3428042
Average (Standard dev.)-0.00013725448 (±0.015647432)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 314.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62223_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_62223_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Cryo-EM of the CUL1-RBX1-SKP1-FBXO3 SCF ubiquition ligase complex

EntireName: Cryo-EM of the CUL1-RBX1-SKP1-FBXO3 SCF ubiquition ligase complex
Components
  • Complex: Cryo-EM of the CUL1-RBX1-SKP1-FBXO3 SCF ubiquition ligase complex
    • Protein or peptide: S-phase kinase-associated protein 1
    • Protein or peptide: F-box only protein 3

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Supramolecule #1: Cryo-EM of the CUL1-RBX1-SKP1-FBXO3 SCF ubiquition ligase complex

SupramoleculeName: Cryo-EM of the CUL1-RBX1-SKP1-FBXO3 SCF ubiquition ligase complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Cryo-EM of the CUL1-RBX1-SKP1-FBXO3 SCF ubiquition ligase complex
Source (natural)Organism: Homo sapiens (human)

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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 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.679965 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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 #2: F-box only protein 3

MacromoleculeName: F-box only protein 3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50.305582 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: METETAPLTL ESLPTDPLLL ILSFLDYRDL INCCYVSRRL SQLSSHDPLW RRHCKKYWLI SEEEKTQKNQ CWKSLFIDTY SDVGRYIDH YAAIKKAWDD LKKYLEPRCP RMVLSLKEGA REEDLDAVEA QIGCKLPDDY RCSYRIHNGQ KLVVPGLLGS M ALSNHYRS ...String:
METETAPLTL ESLPTDPLLL ILSFLDYRDL INCCYVSRRL SQLSSHDPLW RRHCKKYWLI SEEEKTQKNQ CWKSLFIDTY SDVGRYIDH YAAIKKAWDD LKKYLEPRCP RMVLSLKEGA REEDLDAVEA QIGCKLPDDY RCSYRIHNGQ KLVVPGLLGS M ALSNHYRS EDLLDVDTAA GGFQQRQGLK YCLPLTFCIH TGLSQYIAVE AAEGRNKNEV FYQCPDQMAR NPAAIDMFII GA TFTDWFT SYVKNVVSGG FPIIRDQIFR YVHDPECVAT TGDITVSVST SFLPELSSVH PPHYFFTYRI RIEMSKDALP EKA CQLDSR YWRITNAKGD VEEVQGPGVV GEFPIISPGR VYEYTSCTTF STTSGYMEGY YTFHFLYFKD KIFNVAIPRF HMAC PTFRV SIARLEMGPD EYEEMEEEEE EEEEEDEDDD S

UniProtKB: F-box only protein 3

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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
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 55.62 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.9 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.74 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 185640
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9kbf:
Cryo-EM structure of the SKP1-FBXO3 complex

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