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4naw

Crystal Structure of Human ATG12~ATG5-ATG16N in complex with a fragment of ATG3

Method: X-RAY DIFFRACTION Dmax: 142.6 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Ubiquitin-like protein ATG12

Homo sapiens

UniProt O94817

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 52–140 Fragment：UNP residues 52-140 Autophagy protein 5 × 1 （Q9H1Y0） Autophagy-related protein 16-1 × 1 （Q676U5） Ubiquitin-like-conjugating enzyme ATG3 × 1 （Q9NT62） 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
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain E； UniProt 52–140 Fragment：UNP residues 52-140 Autophagy protein 5 × 1 （Q9H1Y0） Autophagy-related protein 16-1 × 1 （Q676U5） Ubiquitin-like-conjugating enzyme ATG3 × 1 （Q9NT62） 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
3 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain I； UniProt 52–140 Fragment：UNP residues 52-140 Autophagy protein 5 × 1 （Q9H1Y0） Autophagy-related protein 16-1 × 1 （Q676U5） Ubiquitin-like-conjugating enzyme ATG3 × 1 （Q9NT62） 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
4 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain M； UniProt 52–140 Fragment：UNP residues 52-140 Autophagy protein 5 × 1 （Q9H1Y0） Autophagy-related protein 16-1 × 1 （Q676U5） Ubiquitin-like-conjugating enzyme ATG3 × 1 （Q9NT62） 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

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 4NAW 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 A 52–140（89 aa）
Chain D 52–140（89 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 construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 52–140（89 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

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

View Construct and Data Evidence
UniProt name ATG12_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–91； UniProt 52–140 Author chain E； PDBConstruct 3–91； UniProt 52–140 Author chain I； PDBConstruct 3–91； UniProt 52–140 Author chain M； PDBConstruct 3–91； UniProt 52–140

Autophagy protein 5

Homo sapiens

UniProt Q9H1Y0

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain B； UniProt 1–275 Not recorded Ubiquitin-like protein ATG12 × 1 （O94817） Autophagy-related protein 16-1 × 1 （Q676U5） Ubiquitin-like-conjugating enzyme ATG3 × 1 （Q9NT62） 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
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain F； UniProt 1–275 Not recorded Ubiquitin-like protein ATG12 × 1 （O94817） Autophagy-related protein 16-1 × 1 （Q676U5） Ubiquitin-like-conjugating enzyme ATG3 × 1 （Q9NT62） 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
3 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain J； UniProt 1–275 Not recorded Ubiquitin-like protein ATG12 × 1 （O94817） Autophagy-related protein 16-1 × 1 （Q676U5） Ubiquitin-like-conjugating enzyme ATG3 × 1 （Q9NT62） 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
4 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain N； UniProt 1–275 Not recorded Ubiquitin-like protein ATG12 × 1 （O94817） Autophagy-related protein 16-1 × 1 （Q676U5） Ubiquitin-like-conjugating enzyme ATG3 × 1 （Q9NT62） 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

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 4NAW 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
4TQ0 Crystal structure of human ATG5-ATG16N69 Deposited 2014-06-10 Different oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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
4TQ1 Crystal structure of human ATG5-TECAIR Deposited 2014-06-10 Different oligomeric state Different ligand/ion 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；277 K；MPD, PEG 1000, PEG 3350, alcohols, MES-imdazole
Resolution 1.80 Å R-free 0.222
5D7G Structure of human ATG5 E122D-ATG16L1 complex at 3.0 Angstroms Deposited 2015-08-13 Different construct Different mutation/modification Different ligand/ion 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 ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ATG5_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–275； UniProt 1–275 Author chain F； PDBConstruct 1–275； UniProt 1–275 Author chain J； PDBConstruct 1–275； UniProt 1–275 Author chain N； PDBConstruct 1–275； UniProt 1–275

Autophagy-related protein 16-1

Homo sapiens

UniProt Q676U5

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain C； UniProt 11–43 Fragment：UNP residues 11-43 Ubiquitin-like protein ATG12 × 1 （O94817） Autophagy protein 5 × 1 （Q9H1Y0） Ubiquitin-like-conjugating enzyme ATG3 × 1 （Q9NT62） 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
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain G； UniProt 11–43 Fragment：UNP residues 11-43 Ubiquitin-like protein ATG12 × 1 （O94817） Autophagy protein 5 × 1 （Q9H1Y0） Ubiquitin-like-conjugating enzyme ATG3 × 1 （Q9NT62） 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
3 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain K； UniProt 11–43 Fragment：UNP residues 11-43 Ubiquitin-like protein ATG12 × 1 （O94817） Autophagy protein 5 × 1 （Q9H1Y0） Ubiquitin-like-conjugating enzyme ATG3 × 1 （Q9NT62） 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
4 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain O； UniProt 11–43 Fragment：UNP residues 11-43 Ubiquitin-like protein ATG12 × 1 （O94817） Autophagy protein 5 × 1 （Q9H1Y0） Ubiquitin-like-conjugating enzyme ATG3 × 1 （Q9NT62） 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

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 4NAW 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 C 11–43（33 aa）
Chain F 11–43（33 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 construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 11–43（33 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
4TQ0 Crystal structure of human ATG5-ATG16N69 Deposited 2014-06-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–69（69 aa） Fragment：UNP residues 1-69
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 construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–69（69 aa） Fragment：UNP residues 1-69
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 construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1–69（69 aa） Fragment：UNP residues 1-69
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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–69（69 aa） Fragment：UNP residues 1-69
Chain D 1–69（69 aa） Fragment：UNP residues 1-69
Not recorded 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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain F 1–69（69 aa） Fragment：UNP residues 1-69
Chain H 1–69（69 aa） Fragment：UNP residues 1-69
Not recorded 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 construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 11–307（297 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 construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 11–307（297 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 construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 11–307（297 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 construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 11–307（297 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 construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 11–307（297 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 construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 11–307（297 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
5NUV Structure of the WD40-domain of human ATG16L1 Deposited 2017-05-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 303–607（305 aa）
Mutation：E354A/K355A/Y607P BU3 (R,R)-2,3-BUTANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.3；303 K；1.61 M (NH4)2SO4, 0.09 M NaCl, 0.1 M MES pH 6.3
Resolution 1.55 Å R-free 0.197
7W36 Crystal structure of human Atg5 complexed with a stapled peptide Deposited 2021-11-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 13–33（21 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) 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
7XFR Crystal structure of WIPI2b in complex with the second site of ATG16L1 Deposited 2022-04-02 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 124–188（65 aa）
Chain D 124–188（65 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；0.1 M MES monohydrate(pH 6.5), 12% w/v Polyethylene glycol 20000
Resolution 1.76 Å R-free 0.193
8ZQG Crystal structure of WIPI3 in complex with ATG16L1 Deposited 2024-06-02 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 124–188（65 aa）
Chain D 124–188（65 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.8；289 K；0.02 M Citric acid, 0.08 M BIS-TRIS propane (pH 8.8); 16% w/v Polyethylene glycol 3350
Resolution 2.77 Å R-free 0.233
9H2Q Stabilized complex of Chlamydia trachomatic efector CT622 in complex with human WD40 domain of ATG16L1 Deposited 2024-10-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 303–607（305 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.80 Å
9J54 Crystal structure of FIP200 Claw in complex with ATG16L1 Deposited 2024-08-11 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 235–247（13 aa）
Chain D 235–247（13 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；289 K；10% v/v 2-Propanol, 0.1 M BICINE (pH 8.5), 30% w/v Polyethylene glycol 1500
Resolution 1.61 Å R-free 0.216
9JF2 Crystal structure of GABARAPL1 in complex with ATG16L1 Deposited 2024-09-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 235–247（13 aa）
Not recorded MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；0.1 M Sodium cacodylate (pH 6.5), 40% v/v MPD, 5% w/v PEG 8000
Resolution 1.76 Å R-free 0.215
9JF2 Crystal structure of GABARAPL1 in complex with ATG16L1 Deposited 2024-09-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 235–247（13 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；0.1 M Sodium cacodylate (pH 6.5), 40% v/v MPD, 5% w/v PEG 8000
Resolution 1.76 Å R-free 0.215

13 other PDB entries and 21 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A16L1_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 4–36； UniProt 11–43 Author chain G； PDBConstruct 4–36； UniProt 11–43 Author chain K； PDBConstruct 4–36； UniProt 11–43 Author chain O； PDBConstruct 4–36； UniProt 11–43

Ubiquitin-like-conjugating enzyme ATG3

Homo sapiens

UniProt Q9NT62

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain D； UniProt 140–170 Fragment：UNP residues 140-170 Ubiquitin-like protein ATG12 × 1 （O94817） Autophagy protein 5 × 1 （Q9H1Y0） Autophagy-related protein 16-1 × 1 （Q676U5） 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
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain H； UniProt 140–170 Fragment：UNP residues 140-170 Ubiquitin-like protein ATG12 × 1 （O94817） Autophagy protein 5 × 1 （Q9H1Y0） Autophagy-related protein 16-1 × 1 （Q676U5） 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
3 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain L； UniProt 140–170 Fragment：UNP residues 140-170 Ubiquitin-like protein ATG12 × 1 （O94817） Autophagy protein 5 × 1 （Q9H1Y0） Autophagy-related protein 16-1 × 1 （Q676U5） 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
4 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain P； UniProt 140–170 Fragment：UNP residues 140-170 Ubiquitin-like protein ATG12 × 1 （O94817） Autophagy protein 5 × 1 （Q9H1Y0） Autophagy-related protein 16-1 × 1 （Q676U5） 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

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 4NAW Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8FKM Human Atg3 with deletions of residues 1 to 25 and 90 to 190 Deposited 2022-12-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–314（314 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) NaCl 150；Pressure 1
NMR sample composition 150 mM NaCl, 50 mM HEPES, 2 mM TCEP, 0.5 mM [U-13C; U-15N] human Atg3, 96% H2O/4% D2O | 96% H2O/4% D2O
NMR sample composition 150 mM NaCl, 50 mM HEPES, 2 mM TCEP, 0.5 mM [U-13C; U-15N] human Atg3, 6.5 mg/mL Pf1 phage, 96% H2O/4% D2O | 96% H2O/4% D2O
NMR sample composition 150 mM NaCl, 50 mM HEPES, 2 mM TCEP, 0.5 mM [U-13C; U-15N] human Atg3, 7 % positive gel, 96% H2O/4% D2O | 96% H2O/4% D2O
NMR sample composition 150 mM NaCl, 50 mM HEPES, 2 mM TCEP, 0.5 mM [U-13C; U-15N] human Atg3, 5 % negative gel, 96% H2O/4% D2O | 96% H2O/4% D2O
NMR sample composition 150 mM NaCl, 50 mM HEPES, 2 mM TCEP, 0.5 mM [U-13C; U-15N] human Atg3, 5 % neutral gel, 96% H2O/4% D2O | 96% H2O/4% D2O
NMR sample composition 150 mM NaCl, 50 mM HEPES, 2 mM TCEP, 0.5 mM [U-13C; U-15N] human Atg3, 100% D2O | 100% D2O
NMR sample composition 150 mM NaCl, 50 mM HEPES, 2 mM TCEP, 0.5 mM [U-13C; U-15N] human Atg3, 92% H2O/8% D2O | 92% H2O/8% D2O
Resolution not provided
9E8P Crystal Structure of GABARAP-ATG3 conjugate Deposited 2024-11-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 26–91（66 aa）
Chain A 148–181（34 aa）
Chain A 193–314（122 aa）
Mutation：C264K Mutation：C264K Mutation：C264K SO4 SULFATE ION × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277.15 K；0.1 mM Tris pH8.5, 25%(w/v) PEG3550
Resolution 2.70 Å R-free 0.249
9E8P Crystal Structure of GABARAP-ATG3 conjugate Deposited 2024-11-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 26–91（66 aa）
Chain B 148–181（34 aa）
Chain B 193–314（122 aa）
Mutation：C264K Mutation：C264K Mutation：C264K EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277.15 K；0.1 mM Tris pH8.5, 25%(w/v) PEG3550
Resolution 2.70 Å R-free 0.249

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ATG3_HUMAN
Isoform —
PDB entities 4
Chains and sequence ranges Author chain D； PDBConstruct 4–34； UniProt 140–170 Author chain H； PDBConstruct 4–34； UniProt 140–170 Author chain L； PDBConstruct 4–34； UniProt 140–170 Author chain P； PDBConstruct 4–34； UniProt 140–170

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 4naw

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4naw
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4naw
Deposition date deposition_date2013-10-22
Structure title titleCrystal Structure of Human ATG12~ATG5-ATG16N in complex with a fragment of ATG3
Keywords keywordsprotein-protein conjugate, ubiquitin-like protein, autophagy, E3 ligase, PROTEIN TRANSPORT-LIGASE complex; PROTEIN TRANSPORT/LIGASE
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_guinier41.37 Å
Radius of gyration Rg (electron density) rg_electron41.10 Å
Forward intensity I(0) i0504053000.00
Molecular weight molecular_weight189290.0 kDa
Excluded volume excluded_volume239110 ų
Envelope volume envelope_volume324500 ų
Hydration-shell volume shell_volume66119 ų
Envelope diameter envelope_diameter152.4 Å
Shell Rg shell_rg45.91 Å
Envelope Rg envelope_rg41.03 Å
Shape Rg shape_rg41.06 Å
Total Rg total_rg41.50 Å
Total atoms total_atoms26591
Residues n_residues1596
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 dmax142.6 Å
Rg (real space) rg_real41.43 Å
Rg uncertainty (real space) rg_real_error1.35 Å
I(0) (real space) i0_real5.0410e+08
I(0) uncertainty (real space) i0_real_error9.9550e+06
Rg (reciprocal space) rg_reciprocal41.38 Å
I(0) (reciprocal space) i0_reciprocal504000000.0000
Solution quality estimate total_estimate0.8551
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary48.8 Å
Skewness Skewness skewness0.450
Kurtosis Kurtosis kurtosis-0.079
Angular range angular_range— – 0.1900 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha100700000.0000
Real-space data points n_real_points39
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.783; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.763
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

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7. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd4nawa_
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.15.1.0 — automated matches
Domain ID domain_idd4nawe_
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.15.1.0 — automated matches
Domain ID domain_idd4nawi_
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.15.1.0 — automated matches
Domain ID domain_idd4nawm_
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.15.1.0 — automated matches

CATH v4.4 (16 domains)

Domain ID domain_id4nawA00
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_id4nawB01
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_id4nawB02
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily620 —
Domain ID domain_id4nawB03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily190 — Autophagy protein Apg5, helix rich domain
Domain ID domain_id4nawE00
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_id4nawF01
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_id4nawF02
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily620 —
Domain ID domain_id4nawF03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily190 — Autophagy protein Apg5, helix rich domain
Domain ID domain_id4nawI00
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_id4nawJ01
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_id4nawJ02
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily620 —
Domain ID domain_id4nawJ03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily190 — Autophagy protein Apg5, helix rich domain
Domain ID domain_id4nawM00
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_id4nawN01
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_id4nawN02
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily620 —
Domain ID domain_id4nawN03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily190 — Autophagy protein Apg5, helix rich domain
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8. Citations (1)

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9. Files and Curves (10)