8AFI: GABARAP
GABARAP in complex with LIR motif of HsATG3. Determined by X-ray diffraction at 2.66 Å resolution. Released 10 May 2023.
- Method
- X-ray diffraction
- Resolution
- 2.66 Å
- Organism
- Homo sapiens
- Chains
- 16
- Atoms
- 8,557
- Mol. weight
- 131.84 kDa
- Released
- 10 May 2023
Explore 8AFI in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8AFI contains 47 α-helices and 69 β-strands across 16 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
Chains A and E: 6 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-8 | 4 | |
| α-helix | 11-24 | 14 | |
| β-strand | 28-35 | 8 | 1 |
| α-helix | 42-44 | 3 | |
| β-strand | 48-52 | 5 | 1 |
| β-strand | 56 | 1 | 2 |
| α-helix | 57-67 | 11 | |
| β-strand | 77-79 | 3 | 1 |
| α-helix | 84-86 | 3 | |
| β-strand | 90 | 1 | 2 |
| α-helix | 91-98 | 8 | |
| β-strand | 105-110 | 6 | 1 |
Chains B, F and L: 0 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 97-98 | 2 | 1 |
| β-strand | 107-109 | 3 | 1 |
Chain C: 5 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-8 | 4 | |
| α-helix | 11-24 | 14 | |
| β-strand | 28-35 | 8 | 3 |
| β-strand | 48-52 | 5 | 3 |
| β-strand | 56 | 1 | 4 |
| α-helix | 57-67 | 11 | |
| β-strand | 77-79 | 3 | 3 |
| β-strand | 80 | 1 | 5 |
| β-strand | 83 | 1 | 5 |
| α-helix | 84-86 | 3 | |
| β-strand | 90 | 1 | 4 |
| α-helix | 91-98 | 8 | |
| β-strand | 105-110 | 6 | 3 |
Chain D: 1 helix, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 95-96 | 2 | |
| β-strand | 97 | 1 | 3 |
| β-strand | 108-109 | 2 | 3 |
Chains G and I: 6 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-8 | 5 | |
| α-helix | 11-24 | 14 | |
| β-strand | 28-35 | 8 | 7 |
| α-helix | 42-44 | 3 | |
| β-strand | 48-52 | 5 | 7 |
| β-strand | 56 | 1 | 13 |
| α-helix | 57-67 | 11 | |
| β-strand | 77-79 | 3 | 7 |
| β-strand | 80 | 1 | 14 |
| β-strand | 83 | 1 | 14 |
| α-helix | 84-86 | 3 | |
| β-strand | 90 | 1 | 13 |
| α-helix | 91-98 | 8 | |
| β-strand | 105-110 | 6 | 7 |
Chains H, N and P: 0 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| β-strand | 109 | 1 | 7 |
Chain J: 1 helix, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 97-98 | 2 | 8 |
| α-helix | 100-102 | 3 | |
| β-strand | 107-109 | 3 | 8 |
Chain K: 4 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 11-24 | 14 | |
| β-strand | 28-35 | 8 | 11 |
| β-strand | 48-52 | 5 | 11 |
| β-strand | 56 | 1 | 17 |
| α-helix | 57-67 | 11 | |
| β-strand | 77-79 | 3 | 11 |
| α-helix | 84-86 | 3 | |
| β-strand | 90 | 1 | 17 |
| α-helix | 91-98 | 8 | |
| β-strand | 105-110 | 6 | 11 |
2 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Gamma-aminobutyric acid receptor-associated protein | A, C, E, G, I, K, M, O | protein | 115 | Homo sapiens | O95166 (AlphaFold model) |
| Ubiquitin-like-conjugating enzyme ATG3 | B, D, F, H, J, L, N, P | protein | 24 | Homo sapiens | Q9NT62 (AlphaFold model) |
Sequence of entity 1 (A, C, E, G, I, K, M, O), FASTA
>8AFI_1 Gamma-aminobutyric acid receptor-associated protein (chains A, C, E, G, I, K, M, O)
KFVYKEEHPFEKRRSEGEKIRKKYPDRVPVIVEKAPKARIGDLDKKKYLVPSDLTVGQFY
FLIRKRIHLRAEDALFFFVNNVIPPTSATMGQLYQEHHEEDFFLYIAYSDESVYG
Sequence of entity 2 (B, D, F, H, J, L, N, P), FASTA
>8AFI_2 Ubiquitin-like-conjugating enzyme ATG3 (chains B, D, F, H, J, L, N, P)
YSDELEAIIEEDDGDGGWVDTYHG
Primary citation
Semisynthetic LC3 Probes for Autophagy Pathways Reveal a Noncanonical LC3 Interacting Region Motif Crucial for the Enzymatic Activity of Human ATG3. Farnung, J., Muhar, M., Liang, J.R. et al. ACS Cent Sci (2023) 9:1025-1034. DOI 10.1021/acscentsci.3c00009 · PubMed
Other PDB entries of the same protein (UniProt O95166 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 6HYO 1.07 Å, Structure of ULK1 LIR motif bound to GABARAP
- 6YOP 1.1 Å, Structure of SAMM50 LIR bound to GABARAP
- 7ZKR 1.1 Å, Human GABARAP in complex with stapled peptide Pen3-ortho
- 6HYN 1.14 Å, Structure of ATG13 LIR motif bound to GABARAP
- 7AA8 1.25 Å, Structure of SCOC LIR bound to GABARAP
- 6HOG 1.26 Å, Structure of VPS34 LIR motif bound to GABARAP
- 8T2M 1.27 Å, Crystal structure of GABARAP in complex with the LIR of NSs4
- 3D32 1.3 Å, Complex of GABA(A) receptor-associated protein (GABARAP) with a synthetic peptide
- 6HB9 1.3 Å, Crystal structure of the GABARAP in complex with the UBA5 LIR motif
- 7BRQ 1.4 Å, Crystal structure of human FAM134B LIR fused to human GABARAP
- 9I9X 1.42 Å, Human GABARAP in complex with artificial peptide IM-2
- 9HGD 1.5 Å, Crystal structure of human GABARAP in complex with cyclic peptide GAB_D23
Browse structure collections
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