9kbf

Cryo-EM structure of the SKP1-FBXO3 complex

Method: ELECTRON MICROSCOPY Dmax: 107.5 Å Quality: GOOD

1. Protein Identity and Related Structures Protein Identity & Related Structures

S-phase kinase-associated protein 1

Homo sapiens

UniProt P63208

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 1–163 Not recorded F-box only protein 3 × 1 (Q9UK99) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.74 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

71 other PDB entries and 97 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SKP1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain B; PDBConstruct 1–163; UniProt 1–163

F-box only protein 3

Homo sapiens

UniProt Q9UK99

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 4–439 Not recorded S-phase kinase-associated protein 1 × 1 (P63208) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.74 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name FBX3_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain C; PDBConstruct 1–436; UniProt 4–439

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 9kbf

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9kbf
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9kbf
Deposition date deposition_date2024-10-30
Structure title titleCryo-EM structure of the SKP1-FBXO3 complex
Keywords keywordsCryo-EM, PROTEIN BINDING, LIGASE; LIGASE
Experimental Method methodELECTRON MICROSCOPY

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier33.46
Radius of gyration Rg (electron density) rg_electron33.16
Forward intensity I(0) i066451400.00
Molecular weight molecular_weight65198.0 kDa
Excluded volume excluded_volume81621 ų
Envelope volume envelope_volume109160 ų
Hydration-shell volume shell_volume28254 ų
Envelope diameter envelope_diameter109.8
Shell Rg shell_rg38.74
Envelope Rg envelope_rg32.75
Shape Rg shape_rg33.15
Total Rg total_rg33.68
Total atoms total_atoms4587
Residues n_residues569
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax107.5
Rg (real space) rg_real33.57
Rg uncertainty (real space) rg_real_error0.75
I(0) (real space) i0_real6.6450e+07
I(0) uncertainty (real space) i0_real_error1.0480e+06
Rg (reciprocal space) rg_reciprocal33.50
I(0) (reciprocal space) i0_reciprocal66450000.0000
Solution quality estimate total_estimate0.8642
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary27.4
Skewness Skewness skewness0.296
Kurtosis Kurtosis kurtosis-0.754
Angular range angular_range— – 0.2350 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha9592000.0000
Real-space data points n_real_points48
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.897; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.764; Smooth: 0.776

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

8. Citations (1)

9. Files and Curves (10)