5whp

Crystal structure of the segment, NFGTFS, from the A315T familial variant of the low complexity domain of TDP-43, residues 312-317

Method: X-RAY DIFFRACTION Dmax: 25.3 Å Quality: GOOD

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

Segment of 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 312–317 Fragment:UNP residues 312-317 Mutation:A315T No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.6;298 K;100mM sodium acetate 4.6, 200mM ammonium acetate, 30% PEG 4000 Resolution 1.00 Å R-free 0.093

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 1–6; UniProt 312–317

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 5whp

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id5whp
Deposition date deposition_date2017-07-17
Structure title titleCrystal structure of the segment, NFGTFS, from the A315T familial variant of the low complexity domain of TDP-43, residues 312-317
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_guinier6.92
Radius of gyration Rg (electron density) rg_electron5.63
Forward intensity I(0) i023750.80
Molecular weight molecular_weight671.7 kDa
Excluded volume excluded_volume831 ų
Envelope volume envelope_volume937 ų
Hydration-shell volume shell_volume1916 ų
Envelope diameter envelope_diameter20.2
Shell Rg shell_rg9.04
Envelope Rg envelope_rg6.02
Shape Rg shape_rg5.64
Total Rg total_rg7.50
Total atoms total_atoms48
Residues n_residues6
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 dmax25.3
Rg (real space) rg_real6.96
Rg uncertainty (real space) rg_real_error0.32
I(0) (real space) i0_real2.3750e+04
I(0) uncertainty (real space) i0_real_error2.4340e+02
Rg (reciprocal space) rg_reciprocal6.96
I(0) (reciprocal space) i0_reciprocal23750.0000
Solution quality estimate total_estimate0.8356
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary24.4
Skewness Skewness skewness0.445
Kurtosis Kurtosis kurtosis-0.038
Angular range angular_range— – 0.5000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1579.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.792; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.687; Smooth: 0.798

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

8. Citations (1)

9. Files and Curves (10)