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8afi

GABARAP in complex with LIR motif of HsATG3

Method: X-RAY DIFFRACTION
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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 Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 2 Ubiquitin-like-conjugating enzyme ATG3 × 1 （C9JNW8） ACETATE ION × 1 GLYCEROL × 1 water × 1 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 2 Ubiquitin-like-conjugating enzyme ATG3 × 1 （C9JNW8） ACETATE ION × 1 GLYCEROL × 1 water × 1 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 2 Ubiquitin-like-conjugating enzyme ATG3 × 1 （C9JNW8） GLYCEROL × 1 water × 1 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 2 Ubiquitin-like-conjugating enzyme ATG3 × 1 （C9JNW8） GLYCEROL × 1 water × 1 Consistent with protein count
5 Protein heterocomplex Heteromer Protein 2 Ubiquitin-like-conjugating enzyme ATG3 × 1 （C9JNW8） GLYCEROL × 1 water × 1 Consistent with protein count
6 Protein heterocomplex Heteromer Protein 2 Ubiquitin-like-conjugating enzyme ATG3 × 1 （C9JNW8） GLYCEROL × 1 water × 1 Consistent with protein count
7 Protein heterocomplex Heteromer Protein 2 Ubiquitin-like-conjugating enzyme ATG3 × 1 （C9JNW8） water × 1 Consistent with protein count
8 Protein heterocomplex Heteromer Protein 2 Ubiquitin-like-conjugating enzyme ATG3 × 1 （C9JNW8） GLYCEROL × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1gnu 1klv 1km7 1kot 6hb9 7aa8 7ea7 7vec

8 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
3d32 3d32 3dow 3wim 5dps 5dps 5dps 6hog 6hoh 6hoh 6hoj 6hok

77 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name GBRAP_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–115； UniProt 2–116 Author chain C； PDBConstruct 1–115； UniProt 2–116 Author chain E； PDBConstruct 1–115； UniProt 2–116 Author chain G； PDBConstruct 1–115； UniProt 2–116 Author chain I； PDBConstruct 1–115； UniProt 2–116 Author chain K； PDBConstruct 1–115； UniProt 2–116 Author chain M； PDBConstruct 1–115； UniProt 2–116 Author chain O； PDBConstruct 1–115； UniProt 2–116

Ubiquitin-like-conjugating enzyme ATG3

OrganismNot specified

UniProt C9JNW8

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 2 Gamma-aminobutyric acid receptor-associated protein × 1 （O95166） ACETATE ION × 1 GLYCEROL × 1 water × 1 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 2 Gamma-aminobutyric acid receptor-associated protein × 1 （O95166） ACETATE ION × 1 GLYCEROL × 1 water × 1 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 2 Gamma-aminobutyric acid receptor-associated protein × 1 （O95166） GLYCEROL × 1 water × 1 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 2 Gamma-aminobutyric acid receptor-associated protein × 1 （O95166） GLYCEROL × 1 water × 1 Consistent with protein count
5 Protein heterocomplex Heteromer Protein 2 Gamma-aminobutyric acid receptor-associated protein × 1 （O95166） GLYCEROL × 1 water × 1 Consistent with protein count
6 Protein heterocomplex Heteromer Protein 2 Gamma-aminobutyric acid receptor-associated protein × 1 （O95166） GLYCEROL × 1 water × 1 Consistent with protein count
7 Protein heterocomplex Heteromer Protein 2 Gamma-aminobutyric acid receptor-associated protein × 1 （O95166） water × 1 Consistent with protein count
8 Protein heterocomplex Heteromer Protein 2 Gamma-aminobutyric acid receptor-associated protein × 1 （O95166） GLYCEROL × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
8afi 8afi 8afi 8afi 8afi 8afi 8afi 8afi

8 assemblies

View Construct and Data Evidence
UniProt name C9JNW8_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–24； UniProt 3–26 Author chain D； PDBConstruct 1–24； UniProt 3–26 Author chain F； PDBConstruct 1–24； UniProt 3–26 Author chain H； PDBConstruct 1–24； UniProt 3–26 Author chain J； PDBConstruct 1–24； UniProt 3–26 Author chain L； PDBConstruct 1–24； UniProt 3–26 Author chain N； PDBConstruct 1–24； UniProt 3–26 Author chain P； PDBConstruct 1–24； UniProt 3–26

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id8afi
Deposition date deposition_date2022-07-18
Structure title titleGABARAP in complex with LIR motif of HsATG3
Keywords keywordsAutophagy, LIR, ATG3, GABARAP, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

8afi__assembly_6__model_1

Assembly 6 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

8afi__assembly_6__model_1 | I(q)

10-2 10-1 105 106 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

8afi__assembly_6__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）15.41 Å
Rg (electron density)13.91 Å
Total Rg15.22 Å
Atom count1995
Residues122
Excluded volume18318 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 8afi__assembly_1__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 8afi__assembly_2__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 8afi__assembly_3__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 8afi__assembly_4__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
5 1 8afi__assembly_5__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
6 1 8afi__assembly_6__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
7 1 8afi__assembly_7__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
8 1 8afi__assembly_8__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (5)

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id8afiA01
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
Domain ID domain_id8afiC01
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
Domain ID domain_id8afiE01
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
Domain ID domain_id8afiG01
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
Domain ID domain_id8afiI01
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
Domain ID domain_id8afiK01
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
Domain ID domain_id8afiM01
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
Domain ID domain_id8afiO01
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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7. Citations (1)