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6a9x

Crystal Structure of AnkG/GABARAP Complex

Method: X-RAY DIFFRACTION Dmax: 50.3 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Gamma-aminobutyric acid receptor-associated protein

Mus musculus

UniProt Q9DCD6

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 D； UniProt 1–117 Not recorded Ankyrin-3 × 1 （O70511） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7；289 K；2.0 M ammonium citrate tribasic, 0.1 M BIS-TRIS propane buffer Resolution 2.20 Å R-free 0.249

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 6A9X Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5YIR Crystal Structure of AnkB LIR/GABARAP complex Deposited 2017-10-06 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–117（117 aa）
Not recorded NI NICKEL (II) ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；289 K；12% w/v PEG 3350, 5 mM CoCl2, 5 mM NiCl2, 5 mM CdCl2, 5 mM MgCl2, 0.1 M HEPES buffer (pH 7.5)
Resolution 2.75 Å R-free 0.224
5YIR Crystal Structure of AnkB LIR/GABARAP complex Deposited 2017-10-06 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–117（117 aa）
Not recorded NI NICKEL (II) ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；289 K；12% w/v PEG 3350, 5 mM CoCl2, 5 mM NiCl2, 5 mM CdCl2, 5 mM MgCl2, 0.1 M HEPES buffer (pH 7.5)
Resolution 2.75 Å R-free 0.224
5YIR Crystal Structure of AnkB LIR/GABARAP complex Deposited 2017-10-06 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–117（117 aa）
Not recorded NI NICKEL (II) ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；289 K；12% w/v PEG 3350, 5 mM CoCl2, 5 mM NiCl2, 5 mM CdCl2, 5 mM MgCl2, 0.1 M HEPES buffer (pH 7.5)
Resolution 2.75 Å R-free 0.224
7FB5 Crystal structure of FAM134B/GABARAP complex Deposited 2021-07-08 Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–117（117 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；containing 0.1 M bis-tris propane pH 8.0, 2.2 M DL-Malic acid
Resolution 2.84 Å R-free 0.244

2 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GBRAP_MOUSE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain D； PDBConstruct 1–117； UniProt 1–117

Ankyrin-3

Rattus norvegicus

UniProt O70511

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 1987–2010 Not recorded Gamma-aminobutyric acid receptor-associated protein × 1 （Q9DCD6） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7；289 K；2.0 M ammonium citrate tribasic, 0.1 M BIS-TRIS propane buffer Resolution 2.20 Å R-free 0.249

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 6A9X Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5YIP Crystal Structure of AnkG LIR/GABARAPL1 complex Deposited 2017-10-06 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1985–2010（26 aa） Fragment：UNP RESIDUES 1985-2010
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 4.6；289 K；35% w/v Pentaerythritol ethoxylate 797 (15/4 EO/OH), 0.2 M ammonium sulfate, 0.1 M sodium acetate (pH 4.6)
Resolution 1.85 Å R-free 0.222
5YIQ Crystal structure of AnkG LIR/LC3B complex Deposited 2017-10-06 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1985–2010（26 aa） Fragment：UNP RESIDUES 1985-2010
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；289 K；10% v/v 2-propanol, 0.2 M zinc acetate, 0.1 M MES buffer (pH 6.5)
Resolution 2.60 Å R-free 0.259
6M3P Crystal structure of AnkG/beta2-spectrin complex Deposited 2020-03-04 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 975–1465（491 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；289 K；10% w/v polyethylene glycol 6,000, 5% v/v (+/-)-2-methyl-2,4-pentanediol and 0.1 M HEPES pH 7.5
Resolution 3.31 Å R-free 0.295
6M3P Crystal structure of AnkG/beta2-spectrin complex Deposited 2020-03-04 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 975–1465（491 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；289 K；10% w/v polyethylene glycol 6,000, 5% v/v (+/-)-2-methyl-2,4-pentanediol and 0.1 M HEPES pH 7.5
Resolution 3.31 Å R-free 0.295
6M3R Crystal structure of AnkG/beta4-spectrin complex Deposited 2020-03-04 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 975–1465（491 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；289 K；0.8 M potassium sodium tartrate tetrahydrate, 0.1 M Tris, pH 8.5 and 0.5% w/v polyethylene glycol monomethyl ether 5,000
Resolution 4.31 Å R-free 0.295
7XCE Crystal structure of Ankyrin G in complex with neurofascin Deposited 2022-03-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 275–500（226 aa）
Not recorded SO4 SULFATE ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；289.2 K；0.1 M ammonium acetate, 0.1 M Bis-Tris (pH 5.5), 17% w/v polyethylene glycol 10000
Resolution 2.50 Å R-free 0.233

5 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ANK3_RAT
Isoform —
PDB entities 2
Chains and sequence ranges Author chain A； PDBConstruct 1–24； UniProt 1987–2010

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 6a9x

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6a9x
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6a9x
Deposition date deposition_date2018-07-16
Structure title titleCrystal Structure of AnkG/GABARAP Complex
Keywords keywordsPROTEIN BINDING, STRUCTURAL PROTEIN, SIGNALING PROTEIN; PROTEIN BINDING
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_guinier15.74 Å
Radius of gyration Rg (electron density) rg_electron14.23 Å
Forward intensity I(0) i04325080.00
Molecular weight molecular_weight15303.0 kDa
Excluded volume excluded_volume19351 ų
Envelope volume envelope_volume21386 ų
Hydration-shell volume shell_volume12767 ų
Envelope diameter envelope_diameter49.5 Å
Shell Rg shell_rg19.99 Å
Envelope Rg envelope_rg14.55 Å
Shape Rg shape_rg14.20 Å
Total Rg total_rg15.50 Å
Total atoms total_atoms1087
Residues n_residues135
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 dmax50.3 Å
Rg (real space) rg_real15.62 Å
Rg uncertainty (real space) rg_real_error0.25 Å
I(0) (real space) i0_real4.3250e+06
I(0) uncertainty (real space) i0_real_error4.4760e+04
Rg (reciprocal space) rg_reciprocal15.64 Å
I(0) (reciprocal space) i0_reciprocal4325000.0000
Solution quality estimate total_estimate0.7689
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary21.6 Å
Skewness Skewness skewness0.081
Kurtosis Kurtosis kurtosis-0.401
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha954700.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.836; Stabil: 1.000; Sysdev: 0.499; Positv: 1.000; Valcen: 0.996; Smooth: 0.989
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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) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd6a9xd_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.3 — GABARAP-like

CATH v4.4 (1 domains)

Domain ID domain_id6a9xD00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
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8. Citations (1)

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9. Files and Curves (10)