3du7

Tubulin-colchicine-phomopsin A: Stathmin-like domain complex

Method: X-RAY DIFFRACTION Dmax: 175.8 Å Quality: REASONABLE

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

Tubulin alpha-1C chain

OrganismNot specified

UniProt Q3ZCJ7

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 1–449 Chain C; UniProt 1–449 Not recorded Tubulin beta-2B chain × 2 (Q6B856) Stathmin-4 × 1 (P63043) MG MAGNESIUM ION × 2 CN2 2-MERCAPTO-N-[1,2,3,10-TETRAMETHOXY-9-OXO-5,6,7,9-TETRAHYDRO-BENZO[A]HEPTALEN-7-YL]ACETAMIDE × 2 HOS Phomopsin A × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;291 K;PEG, PIPES BUFFER. The crystal of tubulin-colchicine:RB3-SLD complex was soaked with a 0.7mM Phomopsin A solution for 24 hours., pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 4.10 Å R-free 0.265

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.

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TBA1C_BOVIN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–449; UniProt 1–449 Author chain C; PDBConstruct 1–449; UniProt 1–449

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain B; UniProt 1–445 Chain D; UniProt 1–445 Not recorded Tubulin alpha-1C chain × 2 (Q3ZCJ7) Stathmin-4 × 1 (P63043) MG MAGNESIUM ION × 2 CN2 2-MERCAPTO-N-[1,2,3,10-TETRAMETHOXY-9-OXO-5,6,7,9-TETRAHYDRO-BENZO[A]HEPTALEN-7-YL]ACETAMIDE × 2 HOS Phomopsin A × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;291 K;PEG, PIPES BUFFER. The crystal of tubulin-colchicine:RB3-SLD complex was soaked with a 0.7mM Phomopsin A solution for 24 hours., pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 4.10 Å R-free 0.265

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain E; UniProt 49–189 Fragment:RB3 stathmin-like domain 4 Tubulin alpha-1C chain × 2 (Q3ZCJ7) Tubulin beta-2B chain × 2 (Q6B856) MG MAGNESIUM ION × 2 CN2 2-MERCAPTO-N-[1,2,3,10-TETRAMETHOXY-9-OXO-5,6,7,9-TETRAHYDRO-BENZO[A]HEPTALEN-7-YL]ACETAMIDE × 2 HOS Phomopsin A × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;291 K;PEG, PIPES BUFFER. The crystal of tubulin-colchicine:RB3-SLD complex was soaked with a 0.7mM Phomopsin A solution for 24 hours., pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 4.10 Å R-free 0.265

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 2–142; UniProt 49–189

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 3du7

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3du7
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id3du7
Deposition date deposition_date2008-07-17
Structure title titleTubulin-colchicine-phomopsin A: Stathmin-like domain complex
Keywords keywords;alpha-tubulin, beta-tubulin, colchicine, gtpase, microtubule, phomopsin A, stathmin, tubulin, GTP-binding, Nucleotide-binding, Phosphoprotein, 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_guinier51.35
Radius of gyration Rg (electron density) rg_electron52.17
Forward intensity I(0) i0646690000.00
Molecular weight molecular_weight203000.0 kDa
Excluded volume excluded_volume250350 ų
Envelope volume envelope_volume331380 ų
Hydration-shell volume shell_volume59010 ų
Envelope diameter envelope_diameter190.6
Shell Rg shell_rg46.91
Envelope Rg envelope_rg52.78
Shape Rg shape_rg52.19
Total Rg total_rg51.95
Total atoms total_atoms14258
Residues n_residues1839
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 dmax175.8
Rg (real space) rg_real52.05
Rg uncertainty (real space) rg_real_error2.66
I(0) (real space) i0_real6.4670e+08
I(0) uncertainty (real space) i0_real_error1.2830e+07
Rg (reciprocal space) rg_reciprocal50.76
I(0) (reciprocal space) i0_reciprocal645500000.0000
Solution quality estimate total_estimate0.6649
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary34.0
Skewness Skewness skewness0.663
Kurtosis Kurtosis kurtosis-0.361
Angular range angular_range— – 0.1550 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha156300000.0000
Real-space data points n_real_points32
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.406; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.311; Smooth: 0.120

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (8)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd3du7a1
Class classi — Low resolution protein structures
Fold Fold foldi.10 — Microtubule complexes
Superfamily Superfamily superfamilyi.10.1 — Microtubule complexes
Family Family familyi.10.1.1 — Microtubule complexes
Domain ID domain_idd3du7b1
Class classi — Low resolution protein structures
Fold Fold foldi.10 — Microtubule complexes
Superfamily Superfamily superfamilyi.10.1 — Microtubule complexes
Family Family familyi.10.1.1 — Microtubule complexes
Domain ID domain_idd3du7e1
Class classa — All alpha proteins
Fold Fold folda.137 — Non-globular all-alpha subunits of globular proteins
Superfamily Superfamily superfamilya.137.10 — Stathmin
Family Family familya.137.10.1 — Stathmin
Domain ID domain_idd3du7e2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

8. Citations (1)

9. Files and Curves (10)