8t33

Crystal structure of K46 acetylated GABARAP in complex with the LIR of TP53INP2/DOR

Method: X-RAY DIFFRACTION Dmax: 47.6 Å Quality: REASONABLE

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

Gamma-aminobutyric acid receptor-associated protein

Homo sapiens

UniProt O95166

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 1–117 Non-standard monomer:Yes (specific site not provided by mmCIF) Tumor protein p53-inducible nuclear protein 2 × 1 (Q8IXH6) ZN ZINC ION × 9 ACT ACETATE ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;10 % w/v PEG 3000, 0.2 M Zinc acetate dihydrate, 0.1 M Sodium acetate PH 4.5 Resolution 1.60 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.

41 other PDB entries and 84 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GBRAP_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 3–119; UniProt 1–117

Tumor protein p53-inducible nuclear protein 2

Homo sapiens

UniProt Q8IXH6

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 31–43 Not recorded Gamma-aminobutyric acid receptor-associated protein × 1 (O95166) ZN ZINC ION × 9 ACT ACETATE ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;10 % w/v PEG 3000, 0.2 M Zinc acetate dihydrate, 0.1 M Sodium acetate PH 4.5 Resolution 1.60 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.

5 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name T53I2_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 3–15; UniProt 31–43

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 8t33

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8t33
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8t33
Deposition date deposition_date2023-06-07
Structure title titleCrystal structure of K46 acetylated GABARAP in complex with the LIR of TP53INP2/DOR
Keywords keywordsAutophagy, GABARAP acetylation, DOR LIR, TP53INP2 LIR, PROTEIN BINDING; PROTEIN BINDING
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier15.74
Radius of gyration Rg (electron density) rg_electron14.24
Forward intensity I(0) i04740760.00
Molecular weight molecular_weight15678.0 kDa
Excluded volume excluded_volume19574 ų
Envelope volume envelope_volume21445 ų
Hydration-shell volume shell_volume12782 ų
Envelope diameter envelope_diameter50.6
Shell Rg shell_rg20.09
Envelope Rg envelope_rg14.57
Shape Rg shape_rg14.15
Total Rg total_rg15.67
Total atoms total_atoms1079
Residues n_residues124
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 dmax47.6
Rg (real space) rg_real15.69
Rg uncertainty (real space) rg_real_error0.07
I(0) (real space) i0_real4.6160e+06
I(0) uncertainty (real space) i0_real_error3.7480e+04
Rg (reciprocal space) rg_reciprocal15.64
I(0) (reciprocal space) i0_reciprocal4741000.0000
Solution quality estimate total_estimate0.7159
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary21.7
Skewness Skewness skewness0.137
Kurtosis Kurtosis kurtosis-0.322
Angular range angular_range— – 0.5000 −1
Current regularization parameter α current_alpha10.2500
Highest regularization parameter α highest_alpha963400.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.921; Stabil: 0.936; Sysdev: 0.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.771

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

8. Citations (1)

9. Files and Curves (10)