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8fkm

Human Atg3 with deletions of residues 1 to 25 and 90 to 190

Method: SOLUTION NMR Dmax: 54.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–314 Not recorded No other associated polymer 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

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 8FKM Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4NAW Crystal Structure of Human ATG12~ATG5-ATG16N in complex with a fragment of ATG3 Deposited 2013-10-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 140–170（31 aa） Fragment：UNP residues 140-170
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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain H 140–170（31 aa） Fragment：UNP residues 140-170
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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain L 140–170（31 aa） Fragment：UNP residues 140-170
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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain P 140–170（31 aa） Fragment：UNP residues 140-170
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
9E8P Crystal Structure of GABARAP-ATG3 conjugate Deposited 2024-11-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 method 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 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ATG3_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–189； UniProt 1–314

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 8fkm

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8fkm
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8fkm
Deposition date deposition_date2022-12-21
Structure title titleHuman Atg3 with deletions of residues 1 to 25 and 90 to 190
Keywords keywordsConjugase, Atg3, Autophagy, LIGASE; LIGASE
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier17.28 Å
Radius of gyration Rg (electron density) rg_electron16.75 Å
Forward intensity I(0) i0641501000.00
Molecular weight molecular_weight220560.0 kDa
Excluded volume excluded_volume278190 ų
Envelope volume envelope_volume45744 ų
Hydration-shell volume shell_volume20422 ų
Envelope diameter envelope_diameter59.6 Å
Shell Rg shell_rg25.08 Å
Envelope Rg envelope_rg18.66 Å
Shape Rg shape_rg16.71 Å
Total Rg total_rg17.09 Å
Total atoms total_atoms30900
Residues n_residues1890
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 dmax54.4 Å
Rg (real space) rg_real17.18 Å
Rg uncertainty (real space) rg_real_error0.32 Å
I(0) (real space) i0_real6.4150e+08
I(0) uncertainty (real space) i0_real_error6.9670e+06
Rg (reciprocal space) rg_reciprocal17.19 Å
I(0) (reciprocal space) i0_reciprocal641500000.0000
Solution quality estimate total_estimate0.8186
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary53.7 Å
Skewness Skewness skewness0.147
Kurtosis Kurtosis kurtosis-0.386
Angular range angular_range— – 0.4600 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1159000.0000
Real-space data points n_real_points77
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.882; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id8fkmA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1460 — Yope Regulator; Chain: A,
Homologous superfamily homologous superfamily50 —
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8. Citations (1)

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9. Files and Curves (10)