4ds1

The Structure of a Yeast Dyn2-Nup159 Complex and the Molecular Basis for the Dynein Light Chain - Nuclear Pore Interaction

Method: X-RAY DIFFRACTION Dmax: 53.6 Å Quality: GOOD

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

Dynein light chain 1, cytoplasmic

Saccharomyces cerevisiae

UniProt Q02647

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 A; UniProt 1–92 Chain C; UniProt 1–92 Not recorded Nucleoporin NUP159 × 2 (P40477) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.5;293 K;0.3 M Ammonium acetate, 5% methyl pentanediol (v/v), 35% PEG 4000 (w/v), pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 1.85 Å R-free 0.187

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 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DYL1_YEAST
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 6–97; UniProt 1–92 Author chain C; PDBConstruct 6–97; UniProt 1–92

Nucleoporin NUP159

OrganismNot specified

UniProt P40477

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 B; UniProt 1116–1126 Chain D; UniProt 1116–1126 Fragment:UNP residues 1116-1126 Dynein light chain 1, cytoplasmic × 2 (Q02647) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.5;293 K;0.3 M Ammonium acetate, 5% methyl pentanediol (v/v), 35% PEG 4000 (w/v), pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 1.85 Å R-free 0.187

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.

5 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NU159_YEAST
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–11; UniProt 1116–1126 Author chain D; PDBConstruct 1–11; UniProt 1116–1126

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 4ds1

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4ds1
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4ds1
Deposition date deposition_date2012-02-17
Structure title titleThe Structure of a Yeast Dyn2-Nup159 Complex and the Molecular Basis for the Dynein Light Chain - Nuclear Pore Interaction
Keywords keywordsnucleoporin, Dynein Light Chain fold, Peptide Binding, Nuclear Pore, STRUCTURAL PROTEIN-TRANSPORT PROTEIN complex; STRUCTURAL PROTEIN/TRANSPORT PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier16.81
Radius of gyration Rg (electron density) rg_electron15.67
Forward intensity I(0) i07656580.00
Molecular weight molecular_weight21735.0 kDa
Excluded volume excluded_volume27813 ų
Envelope volume envelope_volume29622 ų
Hydration-shell volume shell_volume15646 ų
Envelope diameter envelope_diameter53.8
Shell Rg shell_rg21.97
Envelope Rg envelope_rg16.05
Shape Rg shape_rg15.61
Total Rg total_rg16.98
Total atoms total_atoms1541
Residues n_residues193
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 dmax53.6
Rg (real space) rg_real16.71
Rg uncertainty (real space) rg_real_error0.30
I(0) (real space) i0_real7.6570e+06
I(0) uncertainty (real space) i0_real_error8.2860e+04
Rg (reciprocal space) rg_reciprocal16.72
I(0) (reciprocal space) i0_reciprocal7657000.0000
Solution quality estimate total_estimate0.8010
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary22.3
Skewness Skewness skewness0.190
Kurtosis Kurtosis kurtosis-0.278
Angular range angular_range— – 0.4750 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2544000.0000
Real-space data points n_real_points78
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.807; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id4ds1A00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology740 — Protein Inhibitor Of Neuronal Nitric Oxide Synthase
Homologous superfamily homologous superfamily10 — Protein Inhibitor Of Neuronal Nitric Oxide Synthase;
Domain ID domain_id4ds1C00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology740 — Protein Inhibitor Of Neuronal Nitric Oxide Synthase
Homologous superfamily homologous superfamily10 — Protein Inhibitor Of Neuronal Nitric Oxide Synthase;

8. Citations (1)

9. Files and Curves (10)