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9r9b

Crystal structure of clathrin heavy chain in complex with a peptidomimetic inhibitor of the TACC3 interaction

Method: X-RAY DIFFRACTION Dmax: 115.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Clathrin heavy chain 1

Rattus norvegicus

UniProt P11442

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 1–574 Not recorded SP-TACC3 × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.3；291 K；20% w/v polyethylene glycol 3350 200 mM tri-potassium citrate Resolution 2.15 Å R-free 0.268

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.

Other PDB Difference from Current Entry 9R9B Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BPO CLATHRIN HEAVY-CHAIN TERMINAL DOMAIN AND LINKER Deposited 1998-08-11 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–494（494 aa） Fragment：TERMINAL DOMAIN AND LINKER
Chain B 1–494（494 aa） Fragment：TERMINAL DOMAIN AND LINKER
Chain C 1–494（494 aa） Fragment：TERMINAL DOMAIN AND LINKER
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；pH 6.5
Resolution 2.60 Å R-free 0.292
1BPO CLATHRIN HEAVY-CHAIN TERMINAL DOMAIN AND LINKER Deposited 1998-08-11 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 1–494（494 aa） Fragment：TERMINAL DOMAIN AND LINKER
Chain B 1–494（494 aa） Fragment：TERMINAL DOMAIN AND LINKER
Chain C 1–494（494 aa） Fragment：TERMINAL DOMAIN AND LINKER
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；pH 6.5
Resolution 2.60 Å R-free 0.292
1BPO CLATHRIN HEAVY-CHAIN TERMINAL DOMAIN AND LINKER Deposited 1998-08-11 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 1–494（494 aa） Fragment：TERMINAL DOMAIN AND LINKER
Chain C 1–494（494 aa） Fragment：TERMINAL DOMAIN AND LINKER
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；pH 6.5
Resolution 2.60 Å R-free 0.292
1BPO CLATHRIN HEAVY-CHAIN TERMINAL DOMAIN AND LINKER Deposited 1998-08-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–494（494 aa） Fragment：TERMINAL DOMAIN AND LINKER
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；pH 6.5
Resolution 2.60 Å R-free 0.292
1C9I PEPTIDE-IN-GROOVE INTERACTIONS LINK TARGET PROTEINS TO THE B-PROPELLER OF CLATHRIN Deposited 1999-08-02 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–359（359 aa） Fragment：N-TERMINAL DOMAIN
Chain B 1–359（359 aa） Fragment：N-TERMINAL DOMAIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；PEG 4000, KOAc, DTT, Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.90 Å R-free 0.269
1C9L PEPTIDE-IN-GROOVE INTERACTIONS LINK TARGET PROTEINS TO THE B-PROPELLER OF CLATHRIN Deposited 1999-08-02 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 3–359（357 aa） Fragment：N-TERMINAL DOMAIN
Chain B 3–359（357 aa） Fragment：N-TERMINAL DOMAIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；PEG 400, KOAc, DTT, Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.90 Å R-free 0.263

3 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CLH1_RAT
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–574； UniProt 1–574

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 9r9b

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9r9b
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9r9b
Deposition date deposition_date2025-05-19
最后修订 last_revision2026-04-08
Structure title titleCrystal structure of clathrin heavy chain in complex with a peptidomimetic inhibitor of the TACC3 interaction
Keywords keywordsMitotic spindle Hydrocarbon stapled peptide Microtubule-binding, CELL CYCLE; CELL CYCLE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier35.60 Å
Radius of gyration Rg (electron density) rg_electron35.70 Å
Forward intensity I(0) i064758300.00
Molecular weight molecular_weight65794.0 kDa
Excluded volume excluded_volume83123 ų
Envelope volume envelope_volume113320 ų
Hydration-shell volume shell_volume28395 ų
Envelope diameter envelope_diameter125.7 Å
Shell Rg shell_rg39.18 Å
Envelope Rg envelope_rg35.31 Å
Shape Rg shape_rg35.68 Å
Total Rg total_rg36.02 Å
Total atoms total_atoms4628
Residues n_residues587
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax115.8 Å
Rg (real space) rg_real36.01 Å
Rg uncertainty (real space) rg_real_error1.27 Å
I(0) (real space) i0_real6.4760e+07
I(0) uncertainty (real space) i0_real_error1.1610e+06
Rg (reciprocal space) rg_reciprocal35.76 Å
I(0) (reciprocal space) i0_reciprocal64740000.0000
Solution quality estimate total_estimate0.7524
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary29.0 Å
Skewness Skewness skewness0.502
Kurtosis Kurtosis kurtosis-0.580
Angular range angular_range— – 0.2200 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha6521000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.709; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.574; Smooth: 0.075
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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9. Files and Curves (10)