3wso

Crystal structure of the Skp1-FBG3 complex

Method: X-RAY DIFFRACTION Dmax: 94.3 Å Quality: GOOD

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

F-box only protein 44

Homo sapiens

UniProt Q9H4M3

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 A; UniProt 1–255 Not recorded S-phase kinase-associated protein 1 × 1 (P63208) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;288 K;8% 2-propanol, 16% PEG4000, 0.1M Na PIPES , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K Resolution 2.60 Å R-free 0.266

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name FBX44_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–255; UniProt 1–255

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 44 × 1 (Q9H4M3) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;288 K;8% 2-propanol, 16% PEG4000, 0.1M Na PIPES , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K Resolution 2.60 Å R-free 0.266

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 2
Chains and sequence ranges Author chain B; PDBConstruct 4–166; UniProt 1–163

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 3wso

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3wso
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3wso
Deposition date deposition_date2014-03-18
Structure title titleCrystal structure of the Skp1-FBG3 complex
Keywords keywordsF-box protein, SCF ubiquitin ligase, Skp1, LIGASE; LIGASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier29.08
Radius of gyration Rg (electron density) rg_electron28.58
Forward intensity I(0) i033064600.00
Molecular weight molecular_weight45384.0 kDa
Excluded volume excluded_volume56990 ų
Envelope volume envelope_volume73401 ų
Hydration-shell volume shell_volume22702 ų
Envelope diameter envelope_diameter98.8
Shell Rg shell_rg33.81
Envelope Rg envelope_rg28.30
Shape Rg shape_rg28.58
Total Rg total_rg29.14
Total atoms total_atoms3205
Residues n_residues391
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 dmax94.3
Rg (real space) rg_real29.25
Rg uncertainty (real space) rg_real_error0.75
I(0) (real space) i0_real3.3060e+07
I(0) uncertainty (real space) i0_real_error5.1290e+05
Rg (reciprocal space) rg_reciprocal29.18
I(0) (reciprocal space) i0_reciprocal33060000.0000
Solution quality estimate total_estimate0.8609
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.0
Skewness Skewness skewness0.379
Kurtosis Kurtosis kurtosis-0.628
Angular range angular_range— – 0.2750 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7532000.0000
Real-space data points n_real_points56
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.862; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.687; Smooth: 0.914

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd3wsob1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.42 — POZ domain
Superfamily Superfamily superfamilyd.42.1 — POZ domain
Family Family familyd.42.1.0 — automated matches
Domain ID domain_idd3wsob2
Class classa — All alpha proteins
Fold Fold folda.157 — Skp1 dimerisation domain-like
Superfamily Superfamily superfamilya.157.1 — Skp1 dimerisation domain-like
Family Family familya.157.1.1 — Skp1 dimerisation domain-like

CATH v4.4 (3 domains)

Domain ID domain_id3wsoA01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1280 — Monooxygenase
Homologous superfamily homologous superfamily50
Domain ID domain_id3wsoA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily260 — Galactose-binding domain-like
Domain ID domain_id3wsoB00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology710 — Potassium Channel Kv1.1; Chain A
Homologous superfamily homologous superfamily10 — Potassium Channel Kv1.1; Chain A

8. Citations (1)

9. Files and Curves (10)