1x79

Crystal structure of human GGA1 GAT domain complexed with the GAT-binding domain of Rabaptin5

Method: X-RAY DIFFRACTION Dmax: 142.3 Å Quality: REASONABLE

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

ADP-ribosylation factor binding protein GGA1

Homo sapiens

UniProt Q9UJY5

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 210–302 Not recorded Rab GTPase binding effector protein 1 × 2 (Q15276) SO4 SULFATE ION × 2 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 9;293 K;AMMONIUM SULFATE, TRIS, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.41 Å R-free 0.283

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.

19 other PDB entries and 39 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GGA1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 6–98; UniProt 210–302

Rab GTPase binding effector protein 1

Homo sapiens

UniProt Q15276

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain B; UniProt 551–661 Chain C; UniProt 551–661 Not recorded ADP-ribosylation factor binding protein GGA1 × 1 (Q9UJY5) SO4 SULFATE ION × 2 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 9;293 K;AMMONIUM SULFATE, TRIS, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.41 Å R-free 0.283

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 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RABE1_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 2–112; UniProt 551–661 Author chain C; PDBConstruct 2–112; UniProt 551–661

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 1x79

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1x79
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1x79
Deposition date deposition_date2004-08-13
Structure title titleCrystal structure of human GGA1 GAT domain complexed with the GAT-binding domain of Rabaptin5
Keywords keywordsRabaptin5, GGA protein, GAT domain, intracellular trafficking, PROTEIN TRANSPORT; PROTEIN TRANSPORT
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier37.79
Radius of gyration Rg (electron density) rg_electron38.81
Forward intensity I(0) i017594400.00
Molecular weight molecular_weight30606.0 kDa
Excluded volume excluded_volume37561 ų
Envelope volume envelope_volume59845 ų
Hydration-shell volume shell_volume16040 ų
Envelope diameter envelope_diameter138.8
Shell Rg shell_rg35.08
Envelope Rg envelope_rg38.94
Shape Rg shape_rg38.76
Total Rg total_rg38.64
Total atoms total_atoms2126
Residues n_residues260
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 dmax142.3
Rg (real space) rg_real39.02
Rg uncertainty (real space) rg_real_error2.14
I(0) (real space) i0_real1.7590e+07
I(0) uncertainty (real space) i0_real_error3.3220e+05
Rg (reciprocal space) rg_reciprocal38.26
I(0) (reciprocal space) i0_reciprocal17580000.0000
Solution quality estimate total_estimate0.6181
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary23.7
Skewness Skewness skewness0.652
Kurtosis Kurtosis kurtosis-0.612
Angular range angular_range— – 0.2100 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1033000.0000
Real-space data points n_real_points43
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.065; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.009; Smooth: 0.827

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd1x79a_
Class classa — All alpha proteins
Fold Fold folda.7 — Spectrin repeat-like
Superfamily Superfamily superfamilya.7.8 — GAT-like domain
Family Family familya.7.8.1 — GAT domain
Domain ID domain_idd1x79b_
Class classh — Coiled coil proteins
Fold Fold foldh.1 — Parallel coiled-coil
Superfamily Superfamily superfamilyh.1.27 — G protein-binding domain
Family Family familyh.1.27.2 — Rabaptin-5
Domain ID domain_idd1x79c_
Class classh — Coiled coil proteins
Fold Fold foldh.1 — Parallel coiled-coil
Superfamily Superfamily superfamilyh.1.27 — G protein-binding domain
Family Family familyh.1.27.2 — Rabaptin-5

CATH v4.4 (3 domains)

Domain ID domain_id1x79A00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily160
Domain ID domain_id1x79B00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily340
Domain ID domain_id1x79C00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily340

8. Citations (1)

9. Files and Curves (10)