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1ygt

Dynein Light Chain TcTex-1

Method: X-RAY DIFFRACTION Dmax: 53.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Cytoplasmic dynein light chain

Drosophila melanogaster

UniProt Q94524

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–111 Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 9.5；293 K；0.1M CHES, pH 9.5, 2.4 M (NH4)2SO4 and 0.1M Li2SO4, vapor diffusion, temperature 293K X-ray crystallization conditions：VAPOR DIFFUSION；pH 9.5；293 K；0.1M CHES, pH 9.5, 2.4 M (NH4)2SO4 and 0.1M Li2SO4, vapor diffusion, temperature 293K Resolution 1.70 Å R-free 0.235

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 1YGT Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2PG1 Structural analysis of a cytoplasmic dynein Light Chain-Intermediate Chain complex Deposited 2007-04-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain F 1–111（111 aa）
Chain G 1–111（111 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；1.8 M - 2.2 M Ammonium Sulfate, 0 - 20 % glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.80 Å R-free 0.253
2PG1 Structural analysis of a cytoplasmic dynein Light Chain-Intermediate Chain complex Deposited 2007-04-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain E 1–111（111 aa）
Chain H 1–111（111 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；1.8 M - 2.2 M Ammonium Sulfate, 0 - 20 % glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.80 Å R-free 0.253
2PG1 Structural analysis of a cytoplasmic dynein Light Chain-Intermediate Chain complex Deposited 2007-04-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain E 1–111（111 aa）
Chain F 1–111（111 aa）
Chain G 1–111（111 aa）
Chain H 1–111（111 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；1.8 M - 2.2 M Ammonium Sulfate, 0 - 20 % glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.80 Å R-free 0.253
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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–111（111 aa）
Chain B 1–111（111 aa）
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 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DYLX_DROME
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–111； UniProt 1–111

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 1ygt

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1ygt
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1ygt
Deposition date deposition_date2005-01-05
Structure title titleDynein Light Chain TcTex-1
Keywords keywordsDomain Swapping, PROTEIN TRANSPORT; PROTEIN TRANSPORT
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier16.09 Å
Radius of gyration Rg (electron density) rg_electron14.96 Å
Forward intensity I(0) i02988800.00
Molecular weight molecular_weight11711.0 kDa
Excluded volume excluded_volume14507 ų
Envelope volume envelope_volume18154 ų
Hydration-shell volume shell_volume10865 ų
Envelope diameter envelope_diameter51.8 Å
Shell Rg shell_rg19.74 Å
Envelope Rg envelope_rg15.43 Å
Shape Rg shape_rg15.01 Å
Total Rg total_rg15.86 Å
Total atoms total_atoms818
Residues n_residues104
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax53.4 Å
Rg (real space) rg_real16.06 Å
Rg uncertainty (real space) rg_real_error0.33 Å
I(0) (real space) i0_real2.9890e+06
I(0) uncertainty (real space) i0_real_error3.3690e+04
Rg (reciprocal space) rg_reciprocal16.07 Å
I(0) (reciprocal space) i0_reciprocal2989000.0000
Solution quality estimate total_estimate0.8097
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary16.9 Å
Skewness Skewness skewness0.267
Kurtosis Kurtosis kurtosis-0.427
Angular range angular_range— – 0.4950 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha636400.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.853; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.963; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id1ygtA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1140 — Ribosomal protein S3 C-terminal domain
Homologous superfamily homologous superfamily40 — Tctex-1
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8. Citations (1)

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9. Files and Curves (10)