Crystal Structure of Human Atg12~Atg5 Conjugate in Complex with an N-terminal Fragment of Atg16L1. Determined by X-ray diffraction at 2.88 Å resolution. Released 5 Dec 2012.
Explore 4GDL in 3D Show helices and sheets RCSB PDB PDBe
4GDL contains 19 α-helices and 23 β-strands across 3 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.
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 54-61 | 8 | 1 |
| α-helix | 66-68 | 3 | |
| β-strand | 72-76 | 5 | 1 |
| β-strand | 80 | 1 | 2 |
| α-helix | 81-91 | 11 | |
| β-strand | 101-104 | 4 | 1 |
| β-strand | 108 | 1 | 1 |
| β-strand | 115 | 1 | 2 |
| α-helix | 116-123 | 8 | |
| β-strand | 125 | 1 | 1 |
| β-strand | 128-134 | 7 | 1 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 4-12 | 9 | |
| β-strand | 15-22 | 8 | 3 |
| α-helix | 31-34 | 4 | |
| β-strand | 35-40 | 6 | 3 |
| α-helix | 45-47 | 3 | |
| α-helix | 51-57 | 7 | |
| β-strand | 69-72 | 4 | 3 |
| β-strand | 75-76 | 2 | 3 |
| α-helix | 83-90 | 8 | |
| α-helix | 95 | 1 | |
| β-strand | 98-103 | 6 | 3 |
| α-helix | 118-137 | 20 | |
| α-helix | 147-158 | 12 | |
| α-helix | 162-169 | 8 | |
| α-helix | 170-173 | 4 | |
| β-strand | 187-190 | 4 | 4 |
| β-strand | 199 | 1 | 4 |
| β-strand | 206 | 1 | 5 |
| α-helix | 211 | 1 | |
| β-strand | 212 | 1 | 5 |
| α-helix | 213 | 1 | |
| β-strand | 214 | 1 | 6 |
| α-helix | 215-222 | 8 | |
| β-strand | 236-239 | 4 | 4 |
| β-strand | 240 | 1 | 7 |
| β-strand | 243 | 1 | 7 |
| β-strand | 250 | 1 | 6 |
| α-helix | 251-257 | 7 | |
| β-strand | 265-271 | 7 | 4 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 12-27 | 16 | |
| α-helix | 29-41 | 13 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Ubiquitin-like protein ATG12 | A | protein | 91 | Homo sapiens | O94817 (AlphaFold model) |
| Autophagy protein 5 | B | protein | 275 | Homo sapiens | Q9H1Y0 (AlphaFold model) |
| Autophagy-related protein 16-1 | C | protein | 36 | Homo sapiens | Q676U5 (AlphaFold model) |
>4GDL_1 Ubiquitin-like protein ATG12 (chains A) GSKKKIDILLKAVGDTPIMKTKKWAVERTRTIQGLIDFIKKFLKLVASEQLFIYVNQSFA PSPDQEVGTLYECFGSDGKLVLHYCKSQAWG
>4GDL_2 Autophagy protein 5 (chains B) MTDDKDVLRDVWFGRIPTCFTLYQDEITEREAEPYYLLLPRVSYLTLVTDKVKKHFQKVM RQEDISEIWFEYEGTPLKWHYPIGLLFDLLASSSALPWNITVHFKSFPEKDLLHCPSKDA IEAHFMSCMKEADALKHKSQVINEMQKKDHKQLWMGLQNDRFDQFWAINRKLMEYPAEEN GFRYIPFRIYQTTTERPFIQKLFRPVAADGQLHTLGDLLKEVCPSAIDPEDGEKKNQVMI HGIEPMLETPLQWLSEHLSYPDNFLHISIIPQPTD
>4GDL_3 Autophagy-related protein 16-1 (chains C) SHMPRWKRHISEQLRRRDRLQRQAFEEIILQYNKLL
Structure of the human ATG12~ATG5 conjugate required for LC3 lipidation in autophagy. Otomo, C., Metlagel, Z., Takaesu, G. et al. Nat Struct Mol Biol (2013) 20:59-66. DOI 10.1038/nsmb.2431 · PubMed
Other PDB entries of the same protein (UniProt O94817 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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