6bjc

TPX2_mini decorated GMPCPP-microtubule

Method: ELECTRON MICROSCOPY Dmax: 230.9 Å Quality: GOOD

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

Tubulin alpha-1B chain

OrganismNot specified

UniProt Q2XVP4

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 × 14 PDB declaration: tetradecameric(14) Consistent with protein copy count Chain A; UniProt 1–451 Chain C; UniProt 1–451 Chain E; UniProt 1–451 Chain J; UniProt 1–451 Chain K; UniProt 1–451 Chain L; UniProt 1–451 Not recorded Tubulin beta chain × 6 (P02554) Targeting protein for Xklp2 × 2 (Q9ULW0) GTP GUANOSINE-5'-TRIPHOSPHATE × 6 MG MAGNESIUM ION × 12 G2P PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 6 ELECTRON MICROSCOPY cryo-EM buffer:pH 6.8;BRB80 cryo-EM vitrification conditions:Cryogen ETHANE;blot for 4 seconds before plunging Resolution 3.30 Å

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.

230 other PDB entries and 243 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TBA1B_PIG
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 Author chain E; PDBConstruct 1–451; UniProt 1–451 Author chain J; PDBConstruct 1–451; UniProt 1–451 Author chain K; PDBConstruct 1–451; UniProt 1–451 Author chain L; PDBConstruct 1–451; UniProt 1–451

Tubulin beta chain

OrganismNot specified

UniProt P02554

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 × 14 PDB declaration: tetradecameric(14) Consistent with protein copy count Chain B; UniProt 1–445 Chain D; UniProt 1–445 Chain F; UniProt 1–445 Chain G; UniProt 1–445 Chain H; UniProt 1–445 Chain I; UniProt 1–445 Not recorded Tubulin alpha-1B chain × 6 (Q2XVP4) Targeting protein for Xklp2 × 2 (Q9ULW0) GTP GUANOSINE-5'-TRIPHOSPHATE × 6 MG MAGNESIUM ION × 12 G2P PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 6 ELECTRON MICROSCOPY cryo-EM buffer:pH 6.8;BRB80 cryo-EM vitrification conditions:Cryogen ETHANE;blot for 4 seconds before plunging Resolution 3.30 Å

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.

137 other PDB entries and 159 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TBB_PIG
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 Author chain F; PDBConstruct 1–445; UniProt 1–445 Author chain G; PDBConstruct 1–445; UniProt 1–445 Author chain H; PDBConstruct 1–445; UniProt 1–445 Author chain I; PDBConstruct 1–445; UniProt 1–445

Targeting protein for Xklp2

Homo sapiens

UniProt Q9ULW0

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 × 14 PDB declaration: tetradecameric(14) Consistent with protein copy count Chain P; UniProt 1–747 Chain T; UniProt 1–747 Not recorded Tubulin alpha-1B chain × 6 (Q2XVP4) Tubulin beta chain × 6 (P02554) GTP GUANOSINE-5'-TRIPHOSPHATE × 6 MG MAGNESIUM ION × 12 G2P PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 6 ELECTRON MICROSCOPY cryo-EM buffer:pH 6.8;BRB80 cryo-EM vitrification conditions:Cryogen ETHANE;blot for 4 seconds before plunging Resolution 3.30 Å

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.

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

View Construct and Data Evidence
UniProt name TPX2_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain P; PDBConstruct 1–747; UniProt 1–747 Author chain T; PDBConstruct 1–747; UniProt 1–747

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 6bjc

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6bjc
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6bjc
Deposition date deposition_date2017-11-05
Structure title titleTPX2_mini decorated GMPCPP-microtubule
Keywords keywordsmitosis, GanGTP, nucleation, CELL CYCLE; CELL CYCLE
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier66.99
Radius of gyration Rg (electron density) rg_electron66.99
Forward intensity I(0) i05063160000.00
Molecular weight molecular_weight586280.0 kDa
Excluded volume excluded_volume726160 ų
Envelope volume envelope_volume1009100 ų
Hydration-shell volume shell_volume124750 ų
Envelope diameter envelope_diameter241.3
Shell Rg shell_rg66.17
Envelope Rg envelope_rg65.83
Shape Rg shape_rg67.00
Total Rg total_rg66.95
Total atoms total_atoms41136
Residues n_residues5204
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 dmax230.9
Rg (real space) rg_real67.01
Rg uncertainty (real space) rg_real_error3.35
I(0) (real space) i0_real5.0630e+09
I(0) uncertainty (real space) i0_real_error1.2190e+08
Rg (reciprocal space) rg_reciprocal66.83
I(0) (reciprocal space) i0_reciprocal5061000000.0000
Solution quality estimate total_estimate0.8730
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary70.3
Skewness Skewness skewness0.261
Kurtosis Kurtosis kurtosis-0.503
Angular range angular_range— – 0.1150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha145600000.0000
Real-space data points n_real_points24
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.867; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.753

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 36 domains

CATH v4.4 (36 domains)

Domain ID domain_id6bjcA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1440 — Tubulin/FtsZ, GTPase domain
Domain ID domain_id6bjcA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily20 — Tubulin/FtsZ, C-terminal domain
Domain ID domain_id6bjcA03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily600 — Helix hairpin bin
Domain ID domain_id6bjcB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1440 — Tubulin/FtsZ, GTPase domain
Domain ID domain_id6bjcB02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily20 — Tubulin/FtsZ, C-terminal domain
Domain ID domain_id6bjcB03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily600 — Helix hairpin bin
Domain ID domain_id6bjcC01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1440 — Tubulin/FtsZ, GTPase domain
Domain ID domain_id6bjcC02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily20 — Tubulin/FtsZ, C-terminal domain
Domain ID domain_id6bjcC03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily600 — Helix hairpin bin
Domain ID domain_id6bjcD01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1440 — Tubulin/FtsZ, GTPase domain
Domain ID domain_id6bjcD02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily20 — Tubulin/FtsZ, C-terminal domain
Domain ID domain_id6bjcD03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily600 — Helix hairpin bin
Domain ID domain_id6bjcE01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1440 — Tubulin/FtsZ, GTPase domain
Domain ID domain_id6bjcE02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily20 — Tubulin/FtsZ, C-terminal domain
Domain ID domain_id6bjcE03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily600 — Helix hairpin bin
Domain ID domain_id6bjcF01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1440 — Tubulin/FtsZ, GTPase domain
Domain ID domain_id6bjcF02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily20 — Tubulin/FtsZ, C-terminal domain
Domain ID domain_id6bjcF03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily600 — Helix hairpin bin
Domain ID domain_id6bjcG01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1440 — Tubulin/FtsZ, GTPase domain
Domain ID domain_id6bjcG02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily20 — Tubulin/FtsZ, C-terminal domain
Domain ID domain_id6bjcG03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily600 — Helix hairpin bin
Domain ID domain_id6bjcH01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1440 — Tubulin/FtsZ, GTPase domain
Domain ID domain_id6bjcH02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily20 — Tubulin/FtsZ, C-terminal domain
Domain ID domain_id6bjcH03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily600 — Helix hairpin bin
Domain ID domain_id6bjcI01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1440 — Tubulin/FtsZ, GTPase domain
Domain ID domain_id6bjcI02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily20 — Tubulin/FtsZ, C-terminal domain
Domain ID domain_id6bjcI03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily600 — Helix hairpin bin
Domain ID domain_id6bjcJ01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1440 — Tubulin/FtsZ, GTPase domain
Domain ID domain_id6bjcJ02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily20 — Tubulin/FtsZ, C-terminal domain
Domain ID domain_id6bjcJ03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily600 — Helix hairpin bin
Domain ID domain_id6bjcK01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1440 — Tubulin/FtsZ, GTPase domain
Domain ID domain_id6bjcK02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily20 — Tubulin/FtsZ, C-terminal domain
Domain ID domain_id6bjcK03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily600 — Helix hairpin bin
Domain ID domain_id6bjcL01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1440 — Tubulin/FtsZ, GTPase domain
Domain ID domain_id6bjcL02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily20 — Tubulin/FtsZ, C-terminal domain
Domain ID domain_id6bjcL03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily600 — Helix hairpin bin

8. Citations (1)

9. Files and Curves (10)