SAXSdb — 4ds1

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

Dynein light chain 1, cytoplasmic

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Nucleoporin NUP159 × 2 （P40477） water × 4	Consistent with protein count

Other States of the Same Protein in the Database

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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Dynein light chain 1, cytoplasmic × 2 （Q02647） water × 4	Consistent with protein count

Other States of the Same Protein in the Database

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4ds1
Deposition date deposition_date	2012-02-17
Structure title title	The Structure of a Yeast Dyn2-Nup159 Complex and the Molecular Basis for the Dynein Light Chain - Nuclear Pore Interaction
Keywords keywords	nucleoporin, Dynein Light Chain fold, Peptide Binding, Nuclear Pore, STRUCTURAL PROTEIN-TRANSPORT PROTEIN complex; STRUCTURAL PROTEIN/TRANSPORT PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

4ds1__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4ds1__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4ds1__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	16.81 Å
Rg (electron density)	15.67 Å
Total Rg	16.98 Å
Atom count	1541
Residues	193
Excluded volume	27813 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4ds1__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Dynein light chain 1, cytoplasmic
Molecular weight formula_weight	10868.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	1758

GPLGSMSDENKSTPIVKASDITDKLKEDILTISKDALDKYQLERDIAGTVKKQLDVKYGNTWHVIVGKNFGSYVTHEKGHFVYFYIGPLAFLVFKTA

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Nucleoporin NUP159
Molecular weight formula_weight	1210.2 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

NYAESGIQTDL

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	217

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	4ds1A00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	740 — Protein Inhibitor Of Neuronal Nitric Oxide Synthase
Homologous superfamily homologous superfamily	10 — Protein Inhibitor Of Neuronal Nitric Oxide Synthase;

Domain ID domain_id	4ds1C00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	740 — Protein Inhibitor Of Neuronal Nitric Oxide Synthase
Homologous superfamily homologous superfamily	10 — Protein Inhibitor Of Neuronal Nitric Oxide Synthase;

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Unit-cell length a length_a	33.869 Å
Unit-cell length b length_b	47.971 Å
Unit-cell length c length_c	110.703 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.851 Å
Low-resolution limit resolution_low	29.249 Å
R factor r_factor	0.1548
R_work r_work	0.1514
R_free r_free	0.1869

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

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

Dynein light chain 1, cytoplasmic

State in the Current Structure

Other States of the Same Protein in the Database

Nucleoporin NUP159

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4ds1__assembly_1__model_1

4ds1__assembly_1__model_1 | I(q)

4ds1__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

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

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

Dynein light chain 1, cytoplasmic

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Nucleoporin NUP159

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4ds1__assembly_1__model_1

4ds1__assembly_1__model_1 | I(q)

4ds1__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)