SAXSdb — 3l9k

▼

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

RE64145p

Drosophila melanogaster

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 1–97	Not recorded	Dynein intermediate chain, cytosolic × 1 （Q24246）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；277.15 K；1 M sodium citrate, 100 mM sodium chloride, 100 mM Tris., pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K	Resolution 3.00 Å R-free 0.249
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1–97	Not recorded	Dynein intermediate chain, cytosolic × 1 （Q24246）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；277.15 K；1 M sodium citrate, 100 mM sodium chloride, 100 mM Tris., pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K	Resolution 3.00 Å R-free 0.249
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1–97	Not recorded	Dynein intermediate chain, cytosolic × 1 （Q24246）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；277.15 K；1 M sodium citrate, 100 mM sodium chloride, 100 mM Tris., pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K	Resolution 3.00 Å R-free 0.249
4	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 1–97	Not recorded	Dynein intermediate chain, cytosolic × 1 （Q24246）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；277.15 K；1 M sodium citrate, 100 mM sodium chloride, 100 mM Tris., pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K	Resolution 3.00 Å R-free 0.249
5	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–97 Chain B； UniProt 1–97	Not recorded	Dynein intermediate chain, cytosolic × 2 （Q24246）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；277.15 K；1 M sodium citrate, 100 mM sodium chloride, 100 mM Tris., pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K	Resolution 3.00 Å R-free 0.249
6	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain C； UniProt 1–97 Chain D； UniProt 1–97	Not recorded	Dynein intermediate chain, cytosolic × 2 （Q24246）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；277.15 K；1 M sodium citrate, 100 mM sodium chloride, 100 mM Tris., pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K	Resolution 3.00 Å R-free 0.249

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 3L9K	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3L7H Insights into dynein assembly from a dynein intermediate chain light chain Roadblock structure Deposited 2009-12-28	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–97（97 aa） Fragment：LC7 Chain C 1–97（97 aa） Fragment：LC7	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277.15 K；20% iso-propanol, 20% PEG 4000, 100 mM sodium citrate., pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K	Resolution 1.95 Å R-free 0.254
3L7H Insights into dynein assembly from a dynein intermediate chain light chain Roadblock structure Deposited 2009-12-28	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–97（97 aa） Fragment：LC7 Chain D 1–97（97 aa） Fragment：LC7	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277.15 K；20% iso-propanol, 20% PEG 4000, 100 mM sodium citrate., pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K	Resolution 1.95 Å R-free 0.254

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

View Construct and Data Evidence

UniProt name	Q7KMS3_DROME
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–97； UniProt 1–97 Author chain B； PDBConstruct 1–97； UniProt 1–97 Author chain C； PDBConstruct 1–97； UniProt 1–97 Author chain D； PDBConstruct 1–97； UniProt 1–97

Dynein intermediate chain, cytosolic

Drosophila melanogaster

UniProt Q24246

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 Y； UniProt 242–279	Not recorded	RE64145p × 1 （Q7KMS3）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；277.15 K；1 M sodium citrate, 100 mM sodium chloride, 100 mM Tris., pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K	Resolution 3.00 Å R-free 0.249
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain Z； UniProt 242–279	Not recorded	RE64145p × 1 （Q7KMS3）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；277.15 K；1 M sodium citrate, 100 mM sodium chloride, 100 mM Tris., pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K	Resolution 3.00 Å R-free 0.249
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain W； UniProt 242–279	Not recorded	RE64145p × 1 （Q7KMS3）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；277.15 K；1 M sodium citrate, 100 mM sodium chloride, 100 mM Tris., pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K	Resolution 3.00 Å R-free 0.249
4	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain X； UniProt 242–279	Not recorded	RE64145p × 1 （Q7KMS3）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；277.15 K；1 M sodium citrate, 100 mM sodium chloride, 100 mM Tris., pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K	Resolution 3.00 Å R-free 0.249
5	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain Y； UniProt 242–279 Chain Z； UniProt 242–279	Not recorded	RE64145p × 2 （Q7KMS3）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；277.15 K；1 M sodium citrate, 100 mM sodium chloride, 100 mM Tris., pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K	Resolution 3.00 Å R-free 0.249
6	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain W； UniProt 242–279 Chain X； UniProt 242–279	Not recorded	RE64145p × 2 （Q7KMS3）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；277.15 K；1 M sodium citrate, 100 mM sodium chloride, 100 mM Tris., pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K	Resolution 3.00 Å R-free 0.249

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 3L9K	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2P2T Crystal structure of dynein light chain LC8 bound to residues 123-138 of intermediate chain IC74 Deposited 2007-03-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 123–138（16 aa）	Not recorded	ACT ACETATE ION × 2 NA SODIUM ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.00 Å R-free 0.296
3FM7 Quaternary Structure of Drosophila melanogaster IC/Tctex-1/LC8; Allosteric Interactions of Dynein Light Chains with Dynein Intermediate Chain Deposited 2008-12-19	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 109–135（27 aa） Fragment：IC, Residues 109-135 Chain D 109–135（27 aa） Fragment：IC, Residues 109-135	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions Hanging Drop；pH 6.5；277.15 K；16% PEG 8K, 100 mM sodium cacodylate, 200 mM calcium acetate, pH 6.5, Hanging Drop, temperature 277.15K	Resolution 3.50 Å R-free 0.275

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

View Construct and Data Evidence

UniProt name	DYIN_DROME
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain W； PDBConstruct 1–38； UniProt 242–279 Author chain X； PDBConstruct 1–38； UniProt 242–279 Author chain Y； PDBConstruct 1–38； UniProt 242–279 Author chain Z； PDBConstruct 1–38； UniProt 242–279

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3l9k
Deposition date deposition_date	2010-01-05
Structure title title	Insights into dynein assembly from a dynein intermediate chain-light chain roadblock structure
Keywords keywords	;dynein, intermediate chain, IC, LC7, light chain 7, km23, roadblock, Hydrolase, Lysosome, Membrane, Microtubule, Motor protein, Nucleus, WD repeat ;; MOTOR PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	28.88 Å
Radius of gyration Rg (electron density) rg_electron	28.34 Å
Forward intensity I(0) i0	59182400.00
Molecular weight molecular_weight	60033.0 kDa
Excluded volume excluded_volume	75289 Å³
Envelope volume envelope_volume	94870 Å³
Hydration-shell volume shell_volume	28940 Å³
Envelope diameter envelope_diameter	101.1 Å
Shell Rg shell_rg	34.28 Å
Envelope Rg envelope_rg	28.33 Å
Shape Rg shape_rg	28.24 Å
Total Rg total_rg	29.23 Å
Total atoms total_atoms	4176
Residues n_residues	528
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

▼

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

Maximum dimension Dmax dmax	97.2 Å
Rg (real space) rg_real	29.01 Å
Rg uncertainty (real space) rg_real_error	0.78 Å
I(0) (real space) i0_real	5.9180e+07
I(0) uncertainty (real space) i0_real_error	9.1310e+05
Rg (reciprocal space) rg_reciprocal	28.95 Å
I(0) (reciprocal space) i0_reciprocal	59180000.0000
Solution quality estimate total_estimate	0.8500
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.3 Å
Skewness Skewness skewness	0.481
Kurtosis Kurtosis kurtosis	-0.256
Angular range angular_range	— – 0.2750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	19690000.0000
Real-space data points n_real_points	56
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.820; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.857; Smooth: 0.731

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	RE64145p
Molecular weight formula_weight	10837.4 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	4180

MSQEVEETLKRIQSHKGVVGTIVVNNEGIPVKSTLDNTTTVQYAGLMSQLADKARSVVRDLDPSNDMTFLRVRSKKHEIMVAPDKDFILIVIQNPTD

来源 Source

来源生物 organism	Drosophila melanogaster
通用名 common_name	Fruit fly
NCBI Class编号 ncbi_taxonomy_id	7227
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Dynein intermediate chain, cytosolic
Molecular weight formula_weight	4488.1 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	W,X,Y,Z

LSEEQKQMIILSENFQRFVVRAGRVIERALSENVDIYT

来源 Source

来源生物 organism	Drosophila melanogaster
通用名 common_name	Fruit fly
NCBI Class编号 ncbi_taxonomy_id	7227
宿主生物 host_organism	Escherichia coli

▼

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3l9ka_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.110 — Profilin-like
Superfamily Superfamily superfamily	d.110.7 — Roadblock/LC7 domain
Family Family family	d.110.7.1 — Roadblock/LC7 domain

Domain ID domain_id	d3l9kb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.110 — Profilin-like
Superfamily Superfamily superfamily	d.110.7 — Roadblock/LC7 domain
Family Family family	d.110.7.1 — Roadblock/LC7 domain

Domain ID domain_id	d3l9kc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.110 — Profilin-like
Superfamily Superfamily superfamily	d.110.7 — Roadblock/LC7 domain
Family Family family	d.110.7.1 — Roadblock/LC7 domain

Domain ID domain_id	d3l9kd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.110 — Profilin-like
Superfamily Superfamily superfamily	d.110.7 — Roadblock/LC7 domain
Family Family family	d.110.7.1 — Roadblock/LC7 domain

CATH v4.4 (4 domains)

Domain ID domain_id	3l9kA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	30 — Dynein light chain 2a, cytoplasmic

Domain ID domain_id	3l9kB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	30 — Dynein light chain 2a, cytoplasmic

Domain ID domain_id	3l9kC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	30 — Dynein light chain 2a, cytoplasmic

Domain ID domain_id	3l9kD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	30 — Dynein light chain 2a, cytoplasmic

▶

8. Citations (1)

▶

Unit-cell length a length_a	107.180 Å
Unit-cell length b length_b	107.180 Å
Unit-cell length c length_c	65.410 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 32
Space-group number int_tables_number	145
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	92.800 Å
R factor r_factor	0.2280
R_work r_work	0.2270
R_free r_free	0.2490

fit	/app/data/saxs_computation/l9/3l9k/3l9k.fit
pddf	/app/data/pr_computation/l9/3l9k/3l9k.pr.out
profile	/app/data/saxs_computation/l9/3l9k/3l9k.dat

Insights into dynein assembly from a dynein intermediate chain-light chain roadblock structure

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

RE64145p

State in the Current Structure

Other States of the Same Protein in the Database

Dynein intermediate chain, cytosolic

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)