9dhz

Cryo-EM structure of HURP bound to a microtubule

Method: ELECTRON MICROSCOPY Dmax: 128.5 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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain C; UniProt 1–285 Not recorded Tubulin beta chain × 2 (P02554) Tubulin alpha-1B chain × 2 (Q2XVP4) TA1 TAXOL × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 6.9 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.10 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 C; PDBConstruct 7–291; UniProt 1–285

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 1–445 Chain K; UniProt 1–445 Not recorded Disks large-associated protein 5 × 1 (Q15398) Tubulin alpha-1B chain × 2 (Q2XVP4) TA1 TAXOL × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 6.9 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.10 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 A; PDBConstruct 1–445; UniProt 1–445 Author chain K; PDBConstruct 1–445; UniProt 1–445

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain B; UniProt 1–451 Chain L; UniProt 1–451 Not recorded Disks large-associated protein 5 × 1 (Q15398) Tubulin beta chain × 2 (P02554) TA1 TAXOL × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 6.9 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.10 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 B; PDBConstruct 1–451; UniProt 1–451 Author chain L; PDBConstruct 1–451; UniProt 1–451

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 9dhz

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id9dhz
Deposition date deposition_date2024-09-04
最后修订 last_revision2025-07-16
Structure title titleCryo-EM structure of HURP bound to a microtubule
Keywords keywordsHURP, Tubulin, K-fiber, mitosis, spindle, PROTEIN BINDING; PROTEIN BINDING
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier40.20
Radius of gyration Rg (electron density) rg_electron39.70
Forward intensity I(0) i0631216000.00
Molecular weight molecular_weight201630.0 kDa
Excluded volume excluded_volume250060 ų
Envelope volume envelope_volume319000 ų
Hydration-shell volume shell_volume64765 ų
Envelope diameter envelope_diameter137.4
Shell Rg shell_rg47.19
Envelope Rg envelope_rg39.34
Shape Rg shape_rg39.71
Total Rg total_rg40.04
Total atoms total_atoms14150
Residues n_residues1768
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 dmax128.5
Rg (real space) rg_real40.12
Rg uncertainty (real space) rg_real_error1.21
I(0) (real space) i0_real6.3120e+08
I(0) uncertainty (real space) i0_real_error1.2610e+07
Rg (reciprocal space) rg_reciprocal40.20
I(0) (reciprocal space) i0_reciprocal631300000.0000
Solution quality estimate total_estimate0.8948
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary46.1
Skewness Skewness skewness0.222
Kurtosis Kurtosis kurtosis-0.506
Angular range angular_range— – 0.1950 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha211000000.0000
Real-space data points n_real_points40
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.921; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.874

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

8. Citations (1)

9. Files and Curves (10)