← Back to search
9dgp

Motor domain of dynein-1 complex on microtubules

Method: ELECTRON MICROSCOPY Dmax: 161.2 Å Quality: GOOD
▼

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

Cytoplasmic dynein 1 heavy chain 1

OrganismNot specified

UniProt A0A480I0V8

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–4646 Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 4 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.2 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.50 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.

Other PDB Difference from Current Entry 9DGP Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9DGQ Structure of dynein-1 on microtubules Deposited 2024-09-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain m 1–4646（4646 aa）
Chain n 1–4646（4646 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 11.00 Å
9DGR Composite structure of dynein-dynactin on microtubules Deposited 2024-09-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 39 PDB declaration: 39-meric
Chain e 1–4646（4646 aa）
Chain f 1–4646（4646 aa）
Chain m 1–4646（4646 aa）
Chain n 1–4646（4646 aa）
Not recorded ZN ZINC ION × 3 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 15.00 Å
9DGS Dynactin and dynein tail region of dynein-dynactin complex on microtubules Deposited 2024-09-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric
Chain e 1–4646（4646 aa）
Chain f 1–4646（4646 aa）
Chain m 1–4646（4646 aa）
Chain n 1–4646（4646 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 9 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
9DGT structure of dynactin, dynein tail with one BICDR from dynein-dynactin-BICDR on microtubules Deposited 2024-09-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain e 1–4646（4646 aa）
Chain f 1–4646（4646 aa）
Chain m 1–4646（4646 aa）
Chain n 1–4646（4646 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 9 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.20 Å
9DGU structure of dynactin, dynein tail with two BICDR from dynein-dynactin-BICDR on microtubules Deposited 2024-09-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 37 PDB declaration: 37-meric
Chain e 1–4646（4646 aa）
Chain f 1–4646（4646 aa）
Chain m 1–4646（4646 aa）
Chain n 1–4646（4646 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 9 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.10 Å
9DGV structure of dynactin, dynein tail with TRAK2 from dynein-dynactin-TRAK2 on microtubules Deposited 2024-09-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric
Chain e 1–4646（4646 aa）
Chain f 1–4646（4646 aa）
Chain m 1–4646（4646 aa）
Chain n 1–4646（4646 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 9 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.80 Å

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A480I0V8_PIG
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–4646； UniProt 1–4646

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 9dgp

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9dgp
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id9dgp
Deposition date deposition_date2024-09-03
Structure title titleMotor domain of dynein-1 complex on microtubules
Keywords keywordsdynein, microtubule, MOTOR PROTEIN; MOTOR PROTEIN
Experimental Method methodELECTRON MICROSCOPY
▼

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

Radius of gyration Rg (Guinier) rg_guinier49.06 Å
Radius of gyration Rg (electron density) rg_electron48.42 Å
Forward intensity I(0) i01725700000.00
Molecular weight molecular_weight349370.0 kDa
Excluded volume excluded_volume438630 ų
Envelope volume envelope_volume619520 ų
Hydration-shell volume shell_volume102830 ų
Envelope diameter envelope_diameter175.8 Å
Shell Rg shell_rg56.24 Å
Envelope Rg envelope_rg47.19 Å
Shape Rg shape_rg48.43 Å
Total Rg total_rg48.67 Å
Total atoms total_atoms24577
Residues n_residues3037
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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 dmax161.2 Å
Rg (real space) rg_real48.78 Å
Rg uncertainty (real space) rg_real_error1.20 Å
I(0) (real space) i0_real1.7260e+09
I(0) uncertainty (real space) i0_real_error2.8620e+07
Rg (reciprocal space) rg_reciprocal49.06 Å
I(0) (reciprocal space) i0_reciprocal1726000000.0000
Solution quality estimate total_estimate0.8758
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary65.5 Å
Skewness Skewness skewness0.184
Kurtosis Kurtosis kurtosis-0.326
Angular range angular_range— – 0.1600 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha201000000.0000
Real-space data points n_real_points33
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.839; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.884
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (5)

▶

8. Citations (2)

▶

9. Files and Curves (10)