9e0w

Cryo-EM structure of human cytoplasmic dynein-1 bound to LIS1 in the presence of ATP

Method: ELECTRON MICROSCOPY Dmax: 185.0 Å Quality: GOOD

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

Cytoplasmic dynein 1 heavy chain 1

Homo sapiens

UniProt Q14204

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 2–4646 Not recorded Platelet-activating factor acetylhydrolase IB subunit beta × 1 (P43034) ADP ADENOSINE-5'-DIPHOSPHATE × 3 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE-PROPANE Resolution 3.20 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.

96 other PDB entries and 97 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DYHC1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 199–4843; UniProt 2–4646

Platelet-activating factor acetylhydrolase IB subunit beta

Homo sapiens

UniProt P43034

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 2–410 Not recorded Cytoplasmic dynein 1 heavy chain 1 × 1 (Q14204) ADP ADENOSINE-5'-DIPHOSPHATE × 3 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE-PROPANE Resolution 3.20 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.

20 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LIS1_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain C; PDBConstruct 3–411; UniProt 2–410

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 9e0w

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9e0w
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9e0w
Deposition date deposition_date2024-10-20
Structure title titleCryo-EM structure of human cytoplasmic dynein-1 bound to LIS1 in the presence of ATP
Keywords keywordsHuman, MOTOR PROTEIN; MOTOR PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier50.66
Radius of gyration Rg (electron density) rg_electron50.48
Forward intensity I(0) i01722680000.00
Molecular weight molecular_weight348680.0 kDa
Excluded volume excluded_volume437500 ų
Envelope volume envelope_volume627570 ų
Hydration-shell volume shell_volume101670 ų
Envelope diameter envelope_diameter201.0
Shell Rg shell_rg56.06
Envelope Rg envelope_rg50.17
Shape Rg shape_rg50.48
Total Rg total_rg50.66
Total atoms total_atoms24531
Residues n_residues3095
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 dmax185.0
Rg (real space) rg_real50.64
Rg uncertainty (real space) rg_real_error1.87
I(0) (real space) i0_real1.7230e+09
I(0) uncertainty (real space) i0_real_error3.5970e+07
Rg (reciprocal space) rg_reciprocal50.67
I(0) (reciprocal space) i0_reciprocal1723000000.0000
Solution quality estimate total_estimate0.8457
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary59.7
Skewness Skewness skewness0.387
Kurtosis Kurtosis kurtosis-0.017
Angular range angular_range— – 0.1550 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha224100000.0000
Real-space data points n_real_points32
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.682; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.956

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

8. Citations (1)

9. Files and Curves (10)