5wiq

Crystal structure of the segment, GFNGGFG, from the low complexity domain of TDP-43, residues 396-402

Method: X-RAY DIFFRACTION Dmax: 31.0 Å Quality: GOOD

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

TAR DNA-binding protein 43

OrganismNot specified

UniProt Q13148

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 × 10 PDB declaration: decameric(10) Consistent with protein copy count Chain A; UniProt 396–402 Chain B; UniProt 396–402 Fragment:UNP residues 396-402 No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.5;298 K;100mM sodium acetate pH 4.5, 800mM sodium phosphate monobasic, 1200mM potassium phosphate dibasic Resolution 1.25 Å R-free 0.168

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.

41 other PDB entries and 51 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TADBP_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–7; UniProt 396–402 Author chain B; PDBConstruct 1–7; UniProt 396–402

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 5wiq

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5wiq
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5wiq
Deposition date deposition_date2017-07-19
Structure title titleCrystal structure of the segment, GFNGGFG, from the low complexity domain of TDP-43, residues 396-402
Keywords keywordsAmyloid, LARKS, TDP-43, PROTEIN FIBRIL; PROTEIN FIBRIL
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier9.28
Radius of gyration Rg (electron density) rg_electron7.74
Forward intensity I(0) i074841.10
Molecular weight molecular_weight1309.0 kDa
Excluded volume excluded_volume1584 ų
Envelope volume envelope_volume2015 ų
Hydration-shell volume shell_volume2816 ų
Envelope diameter envelope_diameter26.7
Shell Rg shell_rg11.18
Envelope Rg envelope_rg8.08
Shape Rg shape_rg7.66
Total Rg total_rg9.42
Total atoms total_atoms94
Residues n_residues14
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 dmax31.0
Rg (real space) rg_real9.32
Rg uncertainty (real space) rg_real_error0.29
I(0) (real space) i0_real7.4840e+04
I(0) uncertainty (real space) i0_real_error7.7720e+02
Rg (reciprocal space) rg_reciprocal9.32
I(0) (reciprocal space) i0_reciprocal74840.0000
Solution quality estimate total_estimate0.8930
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary10.6
Skewness Skewness skewness0.298
Kurtosis Kurtosis kurtosis-0.414
Angular range angular_range— – 0.5000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha6526.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.934; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.869; Smooth: 0.939

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

8. Citations (1)

9. Files and Curves (10)