SAXSdb — 4ht6

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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	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 1–92	Not recorded	WD repeat-containing protein PAC11 × 1 （P40960）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.8；293 K；0.4M sodium phosphate monobasic, 0.1M 1,6-hexanediol, 25% PEG 3350 (w/v), pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.212
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1–92	Not recorded	WD repeat-containing protein PAC11 × 1 （P40960）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.8；293 K；0.4M sodium phosphate monobasic, 0.1M 1,6-hexanediol, 25% PEG 3350 (w/v), pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.212
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain E； UniProt 1–92	Not recorded	WD repeat-containing protein PAC11 × 1 （P40960）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.8；293 K；0.4M sodium phosphate monobasic, 0.1M 1,6-hexanediol, 25% PEG 3350 (w/v), pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.212
4	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain E； UniProt 1–92	Not recorded	WD repeat-containing protein PAC11 × 2 （P40960）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.8；293 K；0.4M sodium phosphate monobasic, 0.1M 1,6-hexanediol, 25% PEG 3350 (w/v), pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.212

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.

Other PDB	Difference from Current Entry 4HT6	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4DS1 The Structure of a Yeast Dyn2-Nup159 Complex and the Molecular Basis for the Dynein Light Chain - Nuclear Pore Interaction Deposited 2012-02-17	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–92（92 aa） Chain C 1–92（92 aa）	Not recorded	No recorded non-water small molecule	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
7N9F Structure of the in situ yeast NPC Deposited 2021-06-17	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 448 PDB declaration: 448-meric	Chain o 1–92（92 aa） Chain p 1–92（92 aa） Chain q 1–92（92 aa） Chain r 1–92（92 aa） Chain s 1–92（92 aa） Chain t 1–92（92 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；A custom-built vitrification device (Max Planck Institute for Biochemistry, Munich)	Resolution 37.00 Å
7N9F Structure of the in situ yeast NPC Deposited 2021-06-17	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 56 PDB declaration: 56-meric	Chain o 1–92（92 aa） Chain p 1–92（92 aa） Chain q 1–92（92 aa） Chain r 1–92（92 aa） Chain s 1–92（92 aa） Chain t 1–92（92 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；A custom-built vitrification device (Max Planck Institute for Biochemistry, Munich)	Resolution 37.00 Å
7N9F Structure of the in situ yeast NPC Deposited 2021-06-17	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 56 PDB declaration: 56-meric	Chain o 1–92（92 aa） Chain p 1–92（92 aa） Chain q 1–92（92 aa） Chain r 1–92（92 aa） Chain s 1–92（92 aa） Chain t 1–92（92 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；A custom-built vitrification device (Max Planck Institute for Biochemistry, Munich)	Resolution 37.00 Å

2 other PDB entries and 4 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 Author chain E； PDBConstruct 6–97； UniProt 1–92

WD repeat-containing protein PAC11

OrganismNot specified

UniProt P40960

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 B； UniProt 75–85	Fragment：residues 75-85	Dynein light chain 1, cytoplasmic × 1 （Q02647）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.8；293 K；0.4M sodium phosphate monobasic, 0.1M 1,6-hexanediol, 25% PEG 3350 (w/v), pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.212
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 75–85	Fragment：residues 75-85	Dynein light chain 1, cytoplasmic × 1 （Q02647）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.8；293 K；0.4M sodium phosphate monobasic, 0.1M 1,6-hexanediol, 25% PEG 3350 (w/v), pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.212
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain F； UniProt 75–85	Fragment：residues 75-85	Dynein light chain 1, cytoplasmic × 1 （Q02647）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.8；293 K；0.4M sodium phosphate monobasic, 0.1M 1,6-hexanediol, 25% PEG 3350 (w/v), pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.212
4	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain F； UniProt 75–85	Fragment：residues 75-85	Dynein light chain 1, cytoplasmic × 2 （Q02647）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.8；293 K；0.4M sodium phosphate monobasic, 0.1M 1,6-hexanediol, 25% PEG 3350 (w/v), pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.212

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	PAC11_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–11； UniProt 75–85 Author chain D； PDBConstruct 1–11； UniProt 75–85 Author chain F； PDBConstruct 1–11； UniProt 75–85

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	4ht6
Deposition date deposition_date	2012-10-31
Structure title title	The Structure of a Yeast Dynein Dyn2-Pac11 Complex and Effect on Single Molecule Dynein Motor Activity
Keywords keywords	Dimerization, Dynein, Intermediate Chain, Light Chain, Dynein Intermediate Chain Dynein Heavy Chain, MOTOR PROTEIN; MOTOR PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	21.83 Å
Radius of gyration Rg (electron density) rg_electron	21.00 Å
Forward intensity I(0) i0	16677500.00
Molecular weight molecular_weight	33056.0 kDa
Excluded volume excluded_volume	42314 Å³
Envelope volume envelope_volume	48548 Å³
Hydration-shell volume shell_volume	19906 Å³
Envelope diameter envelope_diameter	73.7 Å
Shell Rg shell_rg	27.01 Å
Envelope Rg envelope_rg	21.28 Å
Shape Rg shape_rg	20.96 Å
Total Rg total_rg	22.02 Å
Total atoms total_atoms	2343
Residues n_residues	291
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	74.2 Å
Rg (real space) rg_real	21.87 Å
Rg uncertainty (real space) rg_real_error	0.46 Å
I(0) (real space) i0_real	1.6680e+07
I(0) uncertainty (real space) i0_real_error	2.5660e+05
Rg (reciprocal space) rg_reciprocal	21.87 Å
I(0) (reciprocal space) i0_reciprocal	16680000.0000
Solution quality estimate total_estimate	0.8661
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.3 Å
Skewness Skewness skewness	0.410
Kurtosis Kurtosis kurtosis	-0.315
Angular range angular_range	— – 0.3650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4904000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.784; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.924; Smooth: 0.978

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. 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	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E
Atom count atom_count	2617

GPLGSMSDENKSTPIVKASDITDKLKEDILTISKDALDKYQLERDIAGTVKKQLDVKYGNTWHVIVGKNFGSYVTHEKGHFVYFYIGPLAFLVFKTA

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;Baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	WD repeat-containing protein PAC11
Molecular weight formula_weight	1282.4 kDa
Source method src_method	syn
Copy count entity_count	3

Polymer Polymer

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

ITYDKGIQTDQ

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	274

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	4ht6A00
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	4ht6C00
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	4ht6E00
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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8. Citations (1)

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Unit-cell length a length_a	101.506 Å
Unit-cell length b length_b	112.747 Å
Unit-cell length c length_c	56.369 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	24

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	37.717 Å
R factor r_factor	0.1698
R_work r_work	0.1596
R_free r_free	0.2124

fit	/app/data/saxs_computation/ht/4ht6/4ht6.fit
pddf	/app/data/pr_computation/ht/4ht6/4ht6.pr.out
profile	/app/data/saxs_computation/ht/4ht6/4ht6.dat

The Structure of a Yeast Dynein Dyn2-Pac11 Complex and Effect on Single Molecule Dynein Motor Activity

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

WD repeat-containing protein PAC11

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)