9duq

HURP(65-174) bound to GMPCPP-stabilized microtubule

Method: ELECTRON MICROSCOPY Dmax: 223.1 Å Quality: GOOD

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

Disks large-associated protein 5

Homo sapiens

UniProt Q15398

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 × 27 PDB declaration: 27-meric(27) Consistent with protein copy count Chain r; UniProt 87–132 Chain s; UniProt 87–132 Chain t; UniProt 87–132 Chain u; UniProt 87–132 Chain v; UniProt 87–132 Chain w; UniProt 87–132 Chain x; UniProt 87–132 Chain y; UniProt 87–132 Chain z; UniProt 87–132 Fragment:UNP residues 87-132 Tubulin beta chain × 9 (P02554) Tubulin alpha chain × 9 (Q2XVP4) G2P PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 9 MG MAGNESIUM ION × 18 GTP GUANOSINE-5'-TRIPHOSPHATE × 9 ELECTRON MICROSCOPY cryo-EM buffer:pH 6.8;BRB80 (1X): 80 mM PIPES, 1 mM MgCl2, 1 mM EGTA, pH 6.8 with KOH cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.80 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.

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

View Construct and Data Evidence
UniProt name DLGP5_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain r; PDBConstruct 1–46; UniProt 87–132 Author chain s; PDBConstruct 1–46; UniProt 87–132 Author chain t; PDBConstruct 1–46; UniProt 87–132 Author chain u; PDBConstruct 1–46; UniProt 87–132 Author chain v; PDBConstruct 1–46; UniProt 87–132 Author chain w; PDBConstruct 1–46; UniProt 87–132 Author chain x; PDBConstruct 1–46; UniProt 87–132 Author chain y; PDBConstruct 1–46; UniProt 87–132 Author chain z; PDBConstruct 1–46; UniProt 87–132

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 × 27 PDB declaration: 27-meric(27) Consistent with protein copy count Chain B; UniProt 1–427 Chain D; UniProt 1–427 Chain F; UniProt 1–427 Chain H; UniProt 1–427 Chain J; UniProt 1–427 Chain L; UniProt 1–427 Chain N; UniProt 1–427 Chain P; UniProt 1–427 Chain R; UniProt 1–427 Not recorded Disks large-associated protein 5 × 9 (Q15398) Tubulin alpha chain × 9 (Q2XVP4) G2P PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 9 MG MAGNESIUM ION × 18 GTP GUANOSINE-5'-TRIPHOSPHATE × 9 ELECTRON MICROSCOPY cryo-EM buffer:pH 6.8;BRB80 (1X): 80 mM PIPES, 1 mM MgCl2, 1 mM EGTA, pH 6.8 with KOH cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.80 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 1–427; UniProt 1–427 Author chain D; PDBConstruct 1–427; UniProt 1–427 Author chain F; PDBConstruct 1–427; UniProt 1–427 Author chain H; PDBConstruct 1–427; UniProt 1–427 Author chain J; PDBConstruct 1–427; UniProt 1–427 Author chain L; PDBConstruct 1–427; UniProt 1–427 Author chain N; PDBConstruct 1–427; UniProt 1–427 Author chain P; PDBConstruct 1–427; UniProt 1–427 Author chain R; PDBConstruct 1–427; UniProt 1–427

Tubulin alpha 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 × 27 PDB declaration: 27-meric(27) Consistent with protein copy count Chain A; UniProt 1–439 Chain C; UniProt 1–439 Chain E; UniProt 1–439 Chain G; UniProt 1–439 Chain I; UniProt 1–439 Chain K; UniProt 1–439 Chain M; UniProt 1–439 Chain O; UniProt 1–439 Chain Q; UniProt 1–439 Not recorded Disks large-associated protein 5 × 9 (Q15398) Tubulin beta chain × 9 (P02554) G2P PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 9 MG MAGNESIUM ION × 18 GTP GUANOSINE-5'-TRIPHOSPHATE × 9 ELECTRON MICROSCOPY cryo-EM buffer:pH 6.8;BRB80 (1X): 80 mM PIPES, 1 mM MgCl2, 1 mM EGTA, pH 6.8 with KOH cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.80 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 3
Chains and sequence ranges Author chain A; PDBConstruct 1–439; UniProt 1–439 Author chain C; PDBConstruct 1–439; UniProt 1–439 Author chain E; PDBConstruct 1–439; UniProt 1–439 Author chain G; PDBConstruct 1–439; UniProt 1–439 Author chain I; PDBConstruct 1–439; UniProt 1–439 Author chain K; PDBConstruct 1–439; UniProt 1–439 Author chain M; PDBConstruct 1–439; UniProt 1–439 Author chain O; PDBConstruct 1–439; UniProt 1–439 Author chain Q; PDBConstruct 1–439; UniProt 1–439

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 9duq

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id9duq
Deposition date deposition_date2024-10-03
最后修订 last_revision2024-11-27
Structure title titleHURP(65-174) bound to GMPCPP-stabilized microtubule
Keywords keywordsmicrotubule, nucleation, spindle, oncogene, CELL CYCLE; CELL CYCLE
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier84.21
Radius of gyration Rg (electron density) rg_electron84.79
Forward intensity I(0) i012286800000.00
Molecular weight molecular_weight920020.0 kDa
Excluded volume excluded_volume1140700 ų
Envelope volume envelope_volume1630300 ų
Hydration-shell volume shell_volume163330 ų
Envelope diameter envelope_diameter307.1
Shell Rg shell_rg74.88
Envelope Rg envelope_rg84.15
Shape Rg shape_rg84.79
Total Rg total_rg84.68
Total atoms total_atoms64539
Residues n_residues8127
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 dmax223.1
Rg (real space) rg_real80.78
Rg uncertainty (real space) rg_real_error0.91
I(0) (real space) i0_real1.1930e+10
I(0) uncertainty (real space) i0_real_error2.4170e+08
Rg (reciprocal space) rg_reciprocal82.16
I(0) (reciprocal space) i0_reciprocal12210000000.0000
Solution quality estimate total_estimate0.8920
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary93.9
Skewness Skewness skewness0.294
Kurtosis Kurtosis kurtosis-0.644
Angular range angular_range— – 0.0950 −1
Current regularization parameter α current_alpha0.1037
Highest regularization parameter α highest_alpha295400000.0000
Real-space data points n_real_points20
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.963; Stabil: 0.972; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.046

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

8. Citations (1)

9. Files and Curves (10)