9tdz

Crystal structure of beta-TrCP bound by diphosphorylated claspin degron peptide

Method: X-RAY DIFFRACTION Dmax: 71.9 Å Quality: GOOD

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

F-box/WD repeat-containing protein 1A

Homo sapiens

UniProt Q9Y297

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 222–584 Mutation:L188E, L192E Claspin × 1 (Q9HAW4) EDO 1,2-ETHANEDIOL × 8 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;30% PEG4K, 0.2 M ammonium sulfate, 0.1 M sodium citrate pH 5.6 Resolution 1.35 Å R-free 0.204

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.

14 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name FBW1A_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 3–365; UniProt 222–584

Claspin

Homo sapiens

UniProt Q9HAW4

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 26–37 Non-standard monomer:Yes (specific site not provided by mmCIF) F-box/WD repeat-containing protein 1A × 1 (Q9Y297) EDO 1,2-ETHANEDIOL × 8 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;30% PEG4K, 0.2 M ammonium sulfate, 0.1 M sodium citrate pH 5.6 Resolution 1.35 Å R-free 0.204

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.

4 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CLSPN_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–12; UniProt 26–37

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 9tdz

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id9tdz
Deposition date deposition_date2025-11-24
Structure title titleCrystal structure of beta-TrCP bound by diphosphorylated claspin degron peptide
Keywords keywordsE3 ligase, phosphodegron, beta-TrCP, claspin, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier21.96
Radius of gyration Rg (electron density) rg_electron21.11
Forward intensity I(0) i032363900.00
Molecular weight molecular_weight42453.0 kDa
Excluded volume excluded_volume52532 ų
Envelope volume envelope_volume60036 ų
Hydration-shell volume shell_volume23614 ų
Envelope diameter envelope_diameter73.6
Shell Rg shell_rg28.03
Envelope Rg envelope_rg21.40
Shape Rg shape_rg21.10
Total Rg total_rg21.93
Total atoms total_atoms2974
Residues n_residues364
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 dmax71.9
Rg (real space) rg_real21.89
Rg uncertainty (real space) rg_real_error0.52
I(0) (real space) i0_real3.2360e+07
I(0) uncertainty (real space) i0_real_error4.2070e+05
Rg (reciprocal space) rg_reciprocal21.91
I(0) (reciprocal space) i0_reciprocal32360000.0000
Solution quality estimate total_estimate0.7954
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary29.0
Skewness Skewness skewness0.303
Kurtosis Kurtosis kurtosis-0.264
Angular range angular_range— – 0.3600 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha10200000.0000
Real-space data points n_real_points68
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.808; Stabil: 0.972; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

8. Citations (1)

9. Files and Curves (10)