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9dgq

Structure of dynein-1 on microtubules

Method: ELECTRON MICROSCOPY Dmax: 256.0 Å Quality: EXCELLENT
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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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain m； UniProt 1–4646 Chain n； UniProt 1–4646 Not recorded Dynein light intermediate chain × 2 （A0A8D0X6Z5） 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

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 9DGQ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9DGP Motor domain of dynein-1 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 monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–4646（4646 aa）
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
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 m； PDBConstruct 1–4646； UniProt 1–4646 Author chain n； PDBConstruct 1–4646； UniProt 1–4646

Dynein light intermediate chain

OrganismNot specified

UniProt A0A8D0X6Z5

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain q； UniProt 1–492 Chain r； UniProt 1–492 Not recorded Cytoplasmic dynein 1 heavy chain 1 × 2 （A0A480I0V8） 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

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 9DGQ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
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 i 1–492（492 aa）
Chain j 1–492（492 aa）
Chain q 1–492（492 aa）
Chain r 1–492（492 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
9DGT structure of dynactin, dynein tail with one BICDR from dynein-dynactin-BICDR on microtubules Deposited 2024-09-03 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain j 1–492（492 aa）
Chain q 1–492（492 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 oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 37 PDB declaration: 37-meric
Chain j 1–492（492 aa）
Chain q 1–492（492 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

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

View Construct and Data Evidence
UniProt name A0A8D0X6Z5_PIG
Isoform —
PDB entities 2
Chains and sequence ranges Author chain q； PDBConstruct 1–492； UniProt 1–492 Author chain r； PDBConstruct 1–492； UniProt 1–492

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 9dgq

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id9dgq
Deposition date deposition_date2024-09-03
Structure title titleStructure of dynein-1 on microtubules
Keywords keywordsdynein, microtubule, MOTOR PROTEIN; MOTOR PROTEIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier96.64 Å
Radius of gyration Rg (electron density) rg_electron97.49 Å
Forward intensity I(0) i07818810000.00
Molecular weight molecular_weight462520.0 kDa
Excluded volume excluded_volume454780 ų
Envelope volume envelope_volume1837400 ų
Hydration-shell volume shell_volume172200 ų
Envelope diameter envelope_diameter371.6 Å
Shell Rg shell_rg83.95 Å
Envelope Rg envelope_rg92.13 Å
Shape Rg shape_rg97.52 Å
Total Rg total_rg97.29 Å
Total atoms total_atoms32970
Residues n_residues8153
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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax256.0 Å
Rg (real space) rg_real92.00 Å
Rg uncertainty (real space) rg_real_error0.99 Å
I(0) (real space) i0_real7.4820e+09
I(0) uncertainty (real space) i0_real_error1.4290e+08
Rg (reciprocal space) rg_reciprocal93.69 Å
I(0) (reciprocal space) i0_reciprocal7742000000.0000
Solution quality estimate total_estimate0.9168
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary112.0 Å
Skewness Skewness skewness0.211
Kurtosis Kurtosis kurtosis-0.691
Angular range angular_range— – 0.0800 Å−1
Current regularization parameter α current_alpha0.7426
Highest regularization parameter α highest_alpha443100000.0000
Real-space data points n_real_points17
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.003; Oscil: 0.998; Stabil: 0.975; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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8. Citations (2)

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9. Files and Curves (10)