9gnu

Tubulin in complex with a dioxane analog of zampanolide

Method: X-RAY DIFFRACTION Dmax: 184.5 Å Quality: REASONABLE

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

Tubulin alpha-1B chain

OrganismNot specified

UniProt P81947

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain A; UniProt 1–451 Chain C; UniProt 1–451 Not recorded Tubulin beta-2B chain × 2 (Q6B856) Stathmin-4 × 1 (P63043) Tubulin tyrosine ligase × 1 (A0A8V0Z8P0) GTP GUANOSINE-5'-TRIPHOSPHATE × 3 MG MAGNESIUM ION × 5 CA CALCIUM ION × 4 CL CHLORIDE ION × 1 GOL GLYCEROL × 3 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 A1IND (2Z,4E)-N-((S)-((1R,2E,5S,8E,10Z,14E,17S)-3,11-dimethyl-7,13-dioxo-6,19,21-trioxabicyclo[15.3.1]henicosa-2,8,10,14-tetraen-5-yl)(hydroxy)methyl)hexa-2,4-dienamide × 2 ACP PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;293.15 K;0.1 M Mes / 0.1 M Imidazole pH 6.5, 0.03 M CaCl2 / 0.03 M MgCl2, 5 mM L-Tyrosine, 8 % glycerol, 5.5 % PEG4000 Resolution 2.20 Å R-free 0.206

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.

249 other PDB entries and 251 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TBA1B_BOVIN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–451; UniProt 1–451 Author chain C; PDBConstruct 1–451; UniProt 1–451

Tubulin beta-2B chain

OrganismNot specified

UniProt Q6B856

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain B; UniProt 1–445 Chain D; UniProt 1–445 Not recorded Tubulin alpha-1B chain × 2 (P81947) Stathmin-4 × 1 (P63043) Tubulin tyrosine ligase × 1 (A0A8V0Z8P0) GTP GUANOSINE-5'-TRIPHOSPHATE × 3 MG MAGNESIUM ION × 5 CA CALCIUM ION × 4 CL CHLORIDE ION × 1 GOL GLYCEROL × 3 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 A1IND (2Z,4E)-N-((S)-((1R,2E,5S,8E,10Z,14E,17S)-3,11-dimethyl-7,13-dioxo-6,19,21-trioxabicyclo[15.3.1]henicosa-2,8,10,14-tetraen-5-yl)(hydroxy)methyl)hexa-2,4-dienamide × 2 ACP PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;293.15 K;0.1 M Mes / 0.1 M Imidazole pH 6.5, 0.03 M CaCl2 / 0.03 M MgCl2, 5 mM L-Tyrosine, 8 % glycerol, 5.5 % PEG4000 Resolution 2.20 Å R-free 0.206

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.

273 other PDB entries and 275 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TBB2B_BOVIN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–445; UniProt 1–445 Author chain D; PDBConstruct 1–445; UniProt 1–445

Stathmin-4

Rattus norvegicus

UniProt P63043

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain E; UniProt 1–189 Not recorded Tubulin alpha-1B chain × 2 (P81947) Tubulin beta-2B chain × 2 (Q6B856) Tubulin tyrosine ligase × 1 (A0A8V0Z8P0) GTP GUANOSINE-5'-TRIPHOSPHATE × 3 MG MAGNESIUM ION × 5 CA CALCIUM ION × 4 CL CHLORIDE ION × 1 GOL GLYCEROL × 3 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 A1IND (2Z,4E)-N-((S)-((1R,2E,5S,8E,10Z,14E,17S)-3,11-dimethyl-7,13-dioxo-6,19,21-trioxabicyclo[15.3.1]henicosa-2,8,10,14-tetraen-5-yl)(hydroxy)methyl)hexa-2,4-dienamide × 2 ACP PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;293.15 K;0.1 M Mes / 0.1 M Imidazole pH 6.5, 0.03 M CaCl2 / 0.03 M MgCl2, 5 mM L-Tyrosine, 8 % glycerol, 5.5 % PEG4000 Resolution 2.20 Å R-free 0.206

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.

287 other PDB entries and 287 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name STMN4_RAT
Isoform
PDB entities 3
Chains and sequence ranges Author chain E; PDBConstruct 1–189; UniProt 1–189

Tubulin tyrosine ligase

Gallus gallus

UniProt A0A8V0Z8P0

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain F; UniProt 1–411 Not recorded Tubulin alpha-1B chain × 2 (P81947) Tubulin beta-2B chain × 2 (Q6B856) Stathmin-4 × 1 (P63043) GTP GUANOSINE-5'-TRIPHOSPHATE × 3 MG MAGNESIUM ION × 5 CA CALCIUM ION × 4 CL CHLORIDE ION × 1 GOL GLYCEROL × 3 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 A1IND (2Z,4E)-N-((S)-((1R,2E,5S,8E,10Z,14E,17S)-3,11-dimethyl-7,13-dioxo-6,19,21-trioxabicyclo[15.3.1]henicosa-2,8,10,14-tetraen-5-yl)(hydroxy)methyl)hexa-2,4-dienamide × 2 ACP PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;293.15 K;0.1 M Mes / 0.1 M Imidazole pH 6.5, 0.03 M CaCl2 / 0.03 M MgCl2, 5 mM L-Tyrosine, 8 % glycerol, 5.5 % PEG4000 Resolution 2.20 Å R-free 0.206

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.

25 other PDB entries and 25 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A8V0Z8P0_CHICK
Isoform
PDB entities 4
Chains and sequence ranges Author chain F; PDBConstruct 1–378; UniProt 1–411

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 9gnu

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id9gnu
Deposition date deposition_date2024-09-04
最后修订 last_revision2025-09-17
Structure title titleTubulin in complex with a dioxane analog of zampanolide
Keywords keywordstubulin, zampanolide, microtubule stabilizing agent, CELL CYCLE; CELL CYCLE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier55.86
Radius of gyration Rg (electron density) rg_electron56.75
Forward intensity I(0) i0900391000.00
Molecular weight molecular_weight246780.0 kDa
Excluded volume excluded_volume307110 ų
Envelope volume envelope_volume408920 ų
Hydration-shell volume shell_volume66002 ų
Envelope diameter envelope_diameter197.0
Shell Rg shell_rg50.22
Envelope Rg envelope_rg57.05
Shape Rg shape_rg56.74
Total Rg total_rg56.59
Total atoms total_atoms34166
Residues n_residues2152
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 dmax184.5
Rg (real space) rg_real56.61
Rg uncertainty (real space) rg_real_error2.57
I(0) (real space) i0_real9.0040e+08
I(0) uncertainty (real space) i0_real_error1.8510e+07
Rg (reciprocal space) rg_reciprocal55.19
I(0) (reciprocal space) i0_reciprocal898500000.0000
Solution quality estimate total_estimate0.7153
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary39.5
Skewness Skewness skewness0.564
Kurtosis Kurtosis kurtosis-0.551
Angular range angular_range— – 0.1400 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha84690000.0000
Real-space data points n_real_points29
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.573; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.563; Smooth: 0.013

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (14)

8. Citations (1)

9. Files and Curves (10)