4rh7

Crystal structure of human cytoplasmic dynein 2 motor domain in complex with ADP.Vi

Method: X-RAY DIFFRACTION Dmax: 181.9 Å Quality: GOOD

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

Green fluorescent protein/Cytoplasmic dynein 2 heavy chain 1

Homo sapiens

UniProt Q8NCM8

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 1091–4307 Not recorded AOV ADP ORTHOVANADATE × 1 MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;292 K;mixing equal volumes of protein (8mg/ml) and reservoir solution (4-6 % PEG 6000 and 0.1 M Tris pH 8.0), VAPOR DIFFUSION, HANGING DROP, temperature 292K Resolution 3.41 Å R-free 0.285

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.

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DYHC2_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 233–3449; UniProt 1091–4307

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 4rh7

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4rh7
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4rh7
Deposition date deposition_date2014-10-01
Structure title titleCrystal structure of human cytoplasmic dynein 2 motor domain in complex with ADP.Vi
Keywords keywordsAAA+ protein, motor protein, dynein motor domain; MOTOR PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier58.66
Radius of gyration Rg (electron density) rg_electron60.17
Forward intensity I(0) i01533890000.00
Molecular weight molecular_weight323760.0 kDa
Excluded volume excluded_volume403970 ų
Envelope volume envelope_volume633000 ų
Hydration-shell volume shell_volume97843 ų
Envelope diameter envelope_diameter288.0
Shell Rg shell_rg54.97
Envelope Rg envelope_rg72.95
Shape Rg shape_rg60.52
Total Rg total_rg58.77
Total atoms total_atoms22816
Residues n_residues3005
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 dmax181.9
Rg (real space) rg_real51.81
Rg uncertainty (real space) rg_real_error1.23
I(0) (real space) i0_real1.4730e+09
I(0) uncertainty (real space) i0_real_error2.6750e+07
Rg (reciprocal space) rg_reciprocal55.94
I(0) (reciprocal space) i0_reciprocal1519000000.0000
Solution quality estimate total_estimate0.8831
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary60.6
Skewness Skewness skewness0.868
Kurtosis Kurtosis kurtosis1.011
Angular range angular_range— – 0.1350 −1
Current regularization parameter α current_alpha0.3184
Highest regularization parameter α highest_alpha204900000.0000
Real-space data points n_real_points28
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.011; Oscil: 0.578; Stabil: 0.984; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.936

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id4rh7A01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily20

8. Citations (1)

9. Files and Curves (10)