8pqy

Cytoplasmic dynein-1 motor domain bound to LIS1

Method: ELECTRON MICROSCOPY Dmax: 186.2 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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 1–4646 Mutation:R1567E, K1610E Platelet-activating factor acetylhydrolase IB subunit beta × 2 (P43034) ADP ADENOSINE-5'-DIPHOSPHATE × 3 MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.2 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.80 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.

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 1–4646; UniProt 1–4646

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain B; UniProt 1–410 Chain C; UniProt 1–410 Not recorded Cytoplasmic dynein 1 heavy chain 1 × 1 (Q14204) ADP ADENOSINE-5'-DIPHOSPHATE × 3 MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.2 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.80 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.

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 B; PDBConstruct 1–410; UniProt 1–410 Author chain C; PDBConstruct 1–410; UniProt 1–410

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 8pqy

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8pqy
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8pqy
Deposition date deposition_date2023-07-12
Structure title titleCytoplasmic dynein-1 motor domain bound to LIS1
Keywords keywordsDynein, AAA-Atpase, p150, LIS1, MOTOR PROTEIN; MOTOR PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier54.02
Radius of gyration Rg (electron density) rg_electron53.93
Forward intensity I(0) i02220220000.00
Molecular weight molecular_weight396770.0 kDa
Excluded volume excluded_volume497480 ų
Envelope volume envelope_volume707580 ų
Hydration-shell volume shell_volume108500 ų
Envelope diameter envelope_diameter203.9
Shell Rg shell_rg57.96
Envelope Rg envelope_rg52.93
Shape Rg shape_rg53.93
Total Rg total_rg54.07
Total atoms total_atoms27916
Residues n_residues3518
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 dmax186.2
Rg (real space) rg_real54.04
Rg uncertainty (real space) rg_real_error1.69
I(0) (real space) i0_real2.2200e+09
I(0) uncertainty (real space) i0_real_error4.1720e+07
Rg (reciprocal space) rg_reciprocal53.99
I(0) (reciprocal space) i0_reciprocal2220000000.0000
Solution quality estimate total_estimate0.8657
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary64.2
Skewness Skewness skewness0.389
Kurtosis Kurtosis kurtosis-0.234
Angular range angular_range— – 0.1450 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha237700000.0000
Real-space data points n_real_points30
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.810; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.823

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

8. Citations (1)

9. Files and Curves (10)