Autophagy protein 5
Homo sapiens
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 1–275 | Not recorded | Tectonin beta-propeller repeat-containing protein 1 × 1 (Q7Z6L1) | X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;277 K;MPD, PEG 1000, PEG 3350, alcohols, MES-imdazole | Resolution 1.80 Å R-free 0.222 |
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 4TQ1 | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 4GDK Crystal Structure of Human Atg12~Atg5 Conjugate in Complex with an N-terminal Fragment of Atg16L1 Deposited 2012-07-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer;Protein × 6 PDB declaration: hexameric |
Chain B
1–275(275 aa)
Chain E
1–275(275 aa)
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;PROTEIN: 10 MG/ML in 0.01M HEPES pH 7.0, 0.3 M NaCl, 0.001 M DTT; RESERVOIR: 0.1M Hepes pH7.5, 0.2 M lithium citrate, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.70 Å R-free 0.236 |
| 4GDL Crystal Structure of Human Atg12~Atg5 Conjugate in Complex with an N-terminal Fragment of Atg16L1 Deposited 2012-07-31 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer;Protein × 3 PDB declaration: trimeric |
Chain B
1–275(275 aa)
|
Not recorded | NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP;pH 6.5;293 K;PROTEIN: 10 MG/ML in 0.01M HEPES pH 7.0, 0.3 M NaCl, 0.001 M DTT; RESERVOIR: 0.1M BICINE pH9.0, 0.2 M sodium phosphate dibasic, 18% PEG 3350, vapor diffusion, hanging drop, temperature 293K, VAPOR DIFFUSION, HANGING DROP
|
Resolution 2.88 Å R-free 0.254 |
| 4NAW Crystal Structure of Human ATG12~ATG5-ATG16N in complex with a fragment of ATG3 Deposited 2013-10-22 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer;Protein × 4 PDB declaration: tetrameric |
Chain B
1–275(275 aa)
|
Not recorded | SO4 SULFATE ION × 2 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;pH 7.5;293 K;PROTEIN - 10 MG/ML in 0.01M HEPES pH 7.0, 0.15 M NaCl, 0.001 M DTT, RESERVOIR - 0.1M MES pH6.0-6.75, 0.2 M ammonium sulfate, 10-16% PEG 5000 MME, vapor diffusion, sitting drop, temperature 293K
|
Resolution 2.19 Å R-free 0.215 |
| 4NAW Crystal Structure of Human ATG12~ATG5-ATG16N in complex with a fragment of ATG3 Deposited 2013-10-22 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer;Protein × 4 PDB declaration: tetrameric |
Chain F
1–275(275 aa)
|
Not recorded | SO4 SULFATE ION × 2 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;pH 7.5;293 K;PROTEIN - 10 MG/ML in 0.01M HEPES pH 7.0, 0.15 M NaCl, 0.001 M DTT, RESERVOIR - 0.1M MES pH6.0-6.75, 0.2 M ammonium sulfate, 10-16% PEG 5000 MME, vapor diffusion, sitting drop, temperature 293K
|
Resolution 2.19 Å R-free 0.215 |
| 4NAW Crystal Structure of Human ATG12~ATG5-ATG16N in complex with a fragment of ATG3 Deposited 2013-10-22 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer;Protein × 4 PDB declaration: tetrameric |
Chain J
1–275(275 aa)
|
Not recorded | SO4 SULFATE ION × 4 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;pH 7.5;293 K;PROTEIN - 10 MG/ML in 0.01M HEPES pH 7.0, 0.15 M NaCl, 0.001 M DTT, RESERVOIR - 0.1M MES pH6.0-6.75, 0.2 M ammonium sulfate, 10-16% PEG 5000 MME, vapor diffusion, sitting drop, temperature 293K
|
Resolution 2.19 Å R-free 0.215 |
| 4NAW Crystal Structure of Human ATG12~ATG5-ATG16N in complex with a fragment of ATG3 Deposited 2013-10-22 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer;Protein × 4 PDB declaration: tetrameric |
Chain N
1–275(275 aa)
|
Not recorded | SO4 SULFATE ION × 3 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;pH 7.5;293 K;PROTEIN - 10 MG/ML in 0.01M HEPES pH 7.0, 0.15 M NaCl, 0.001 M DTT, RESERVOIR - 0.1M MES pH6.0-6.75, 0.2 M ammonium sulfate, 10-16% PEG 5000 MME, vapor diffusion, sitting drop, temperature 293K
|
Resolution 2.19 Å R-free 0.215 |
| 4TQ0 Crystal structure of human ATG5-ATG16N69 Deposited 2014-06-10 | Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer;Protein × 2 PDB declaration: dimeric |
Chain A
1–275(275 aa)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP;293 K;PEG 400, MgCl2, KCl, Tris-HCl
|
Resolution 2.70 Å R-free 0.274 |
| 4TQ0 Crystal structure of human ATG5-ATG16N69 Deposited 2014-06-10 | Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer;Protein × 2 PDB declaration: dimeric |
Chain C
1–275(275 aa)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP;293 K;PEG 400, MgCl2, KCl, Tris-HCl
|
Resolution 2.70 Å R-free 0.274 |
| 4TQ0 Crystal structure of human ATG5-ATG16N69 Deposited 2014-06-10 | Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer;Protein × 2 PDB declaration: dimeric |
Chain E
1–275(275 aa)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP;293 K;PEG 400, MgCl2, KCl, Tris-HCl
|
Resolution 2.70 Å R-free 0.274 |
| 5D7G Structure of human ATG5 E122D-ATG16L1 complex at 3.0 Angstroms Deposited 2015-08-13 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer;Protein × 4 PDB declaration: tetrameric |
Chain A
1–275(275 aa)
Chain C
1–275(275 aa)
|
Mutation:E122D Mutation:E122D | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP;pH 5.5;277 K;Micro crystal: 37.5 mM MES, pH 5.2 to pH 5.8, 0.2 M sodium tartrate, and 11 to 13% polyethylene glycol 3350; Micor seeding condition:40 mM MES, pH 5.5, 0.2M sodium tartrate, 8.5% PEG3350, 10 mM DTT
|
Resolution 3.00 Å R-free 0.244 |
| 5D7G Structure of human ATG5 E122D-ATG16L1 complex at 3.0 Angstroms Deposited 2015-08-13 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer;Protein × 4 PDB declaration: tetrameric |
Chain E
1–275(275 aa)
Chain G
1–275(275 aa)
|
Mutation:E122D Mutation:E122D | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP;pH 5.5;277 K;Micro crystal: 37.5 mM MES, pH 5.2 to pH 5.8, 0.2 M sodium tartrate, and 11 to 13% polyethylene glycol 3350; Micor seeding condition:40 mM MES, pH 5.5, 0.2M sodium tartrate, 8.5% PEG3350, 10 mM DTT
|
Resolution 3.00 Å R-free 0.244 |
| 5NPV Structure of human ATG5-ATG16L1(ATG5BD) complex (I4) Deposited 2017-04-19 | Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer;Protein × 2 PDB declaration: dimeric |
Chain A
1–275(275 aa)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;pH 5.76;293 K;0.1 M MES pH 5.76, 0.378 M KCl, 21.7 % PEG 3350
|
Resolution 3.10 Å R-free 0.278 |
| 5NPV Structure of human ATG5-ATG16L1(ATG5BD) complex (I4) Deposited 2017-04-19 | Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer;Protein × 2 PDB declaration: dimeric |
Chain C
1–275(275 aa)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;pH 5.76;293 K;0.1 M MES pH 5.76, 0.378 M KCl, 21.7 % PEG 3350
|
Resolution 3.10 Å R-free 0.278 |
| 5NPW Structure of human ATG5-ATG16L1(ATG5BD) complex (C2) Deposited 2017-04-19 | Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer;Protein × 2 PDB declaration: dimeric |
Chain A
1–275(275 aa)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;293 K;0.4 M KCl and 18 % PEG 3350
|
Resolution 3.10 Å R-free 0.264 |
| 5NPW Structure of human ATG5-ATG16L1(ATG5BD) complex (C2) Deposited 2017-04-19 | Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer;Protein × 2 PDB declaration: dimeric |
Chain C
1–275(275 aa)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;293 K;0.4 M KCl and 18 % PEG 3350
|
Resolution 3.10 Å R-free 0.264 |
| 5NPW Structure of human ATG5-ATG16L1(ATG5BD) complex (C2) Deposited 2017-04-19 | Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer;Protein × 2 PDB declaration: dimeric |
Chain E
1–275(275 aa)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;293 K;0.4 M KCl and 18 % PEG 3350
|
Resolution 3.10 Å R-free 0.264 |
| 5NPW Structure of human ATG5-ATG16L1(ATG5BD) complex (C2) Deposited 2017-04-19 | Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer;Protein × 2 PDB declaration: dimeric |
Chain G
1–275(275 aa)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;293 K;0.4 M KCl and 18 % PEG 3350
|
Resolution 3.10 Å R-free 0.264 |
| 7W36 Crystal structure of human Atg5 complexed with a stapled peptide Deposited 2021-11-25 | Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer;Protein × 2 PDB declaration: dimeric |
Chain A
1–275(275 aa)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;293 K;20% PEG 3350, 0.2M MgCl2, 0.1M Tris-HCl pH8.5
|
Resolution 3.00 Å R-free 0.287 |
8 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | ATG5_HUMAN |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A; PDBConstruct 15–289; UniProt 1–275 |