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4naw

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

Method: X-RAY DIFFRACTION
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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 Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 4 Autophagy protein 5 × 1 （Q9H1Y0） Autophagy-related protein 16-1 × 1 （Q676U5） Ubiquitin-like-conjugating enzyme ATG3 × 1 （Q9NT62） SULFATE ION × 2 SODIUM ION × 1 water × 3 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 4 Autophagy protein 5 × 1 （Q9H1Y0） Autophagy-related protein 16-1 × 1 （Q676U5） Ubiquitin-like-conjugating enzyme ATG3 × 1 （Q9NT62） SULFATE ION × 2 SODIUM ION × 1 water × 3 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 4 Autophagy protein 5 × 1 （Q9H1Y0） Autophagy-related protein 16-1 × 1 （Q676U5） Ubiquitin-like-conjugating enzyme ATG3 × 1 （Q9NT62） SULFATE ION × 4 SODIUM ION × 1 water × 4 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 4 Autophagy protein 5 × 1 （Q9H1Y0） Autophagy-related protein 16-1 × 1 （Q676U5） Ubiquitin-like-conjugating enzyme ATG3 × 1 （Q9NT62） SULFATE ION × 3 SODIUM ION × 1 water × 3 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
4gdk 4gdl 4naw 4naw 4naw 4naw

6 assemblies

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 Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 4 Ubiquitin-like protein ATG12 × 1 （O94817） Autophagy-related protein 16-1 × 1 （Q676U5） Ubiquitin-like-conjugating enzyme ATG3 × 1 （Q9NT62） SULFATE ION × 2 SODIUM ION × 1 water × 3 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 4 Ubiquitin-like protein ATG12 × 1 （O94817） Autophagy-related protein 16-1 × 1 （Q676U5） Ubiquitin-like-conjugating enzyme ATG3 × 1 （Q9NT62） SULFATE ION × 2 SODIUM ION × 1 water × 3 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 4 Ubiquitin-like protein ATG12 × 1 （O94817） Autophagy-related protein 16-1 × 1 （Q676U5） Ubiquitin-like-conjugating enzyme ATG3 × 1 （Q9NT62） SULFATE ION × 4 SODIUM ION × 1 water × 4 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 4 Ubiquitin-like protein ATG12 × 1 （O94817） Autophagy-related protein 16-1 × 1 （Q676U5） Ubiquitin-like-conjugating enzyme ATG3 × 1 （Q9NT62） SULFATE ION × 3 SODIUM ION × 1 water × 3 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
4gdk 4gdl 4naw 4naw 4naw 4naw 4tq0 4tq0 4tq0 4tq1 5d7g 5d7g

19 assemblies; showing the first 12

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 Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 4 Ubiquitin-like protein ATG12 × 1 （O94817） Autophagy protein 5 × 1 （Q9H1Y0） Ubiquitin-like-conjugating enzyme ATG3 × 1 （Q9NT62） SULFATE ION × 2 SODIUM ION × 1 water × 3 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 4 Ubiquitin-like protein ATG12 × 1 （O94817） Autophagy protein 5 × 1 （Q9H1Y0） Ubiquitin-like-conjugating enzyme ATG3 × 1 （Q9NT62） SULFATE ION × 2 SODIUM ION × 1 water × 3 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 4 Ubiquitin-like protein ATG12 × 1 （O94817） Autophagy protein 5 × 1 （Q9H1Y0） Ubiquitin-like-conjugating enzyme ATG3 × 1 （Q9NT62） SULFATE ION × 4 SODIUM ION × 1 water × 4 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 4 Ubiquitin-like protein ATG12 × 1 （O94817） Autophagy protein 5 × 1 （Q9H1Y0） Ubiquitin-like-conjugating enzyme ATG3 × 1 （Q9NT62） SULFATE ION × 3 SODIUM ION × 1 water × 3 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
5nuv

1 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
4gdk 4gdl 4naw 4naw 4naw 4naw 4tq0 4tq0 4tq0 5d7g 5d7g 5npv

24 assemblies; showing the first 12

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 Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 4 Ubiquitin-like protein ATG12 × 1 （O94817） Autophagy protein 5 × 1 （Q9H1Y0） Autophagy-related protein 16-1 × 1 （Q676U5） SULFATE ION × 2 SODIUM ION × 1 water × 3 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 4 Ubiquitin-like protein ATG12 × 1 （O94817） Autophagy protein 5 × 1 （Q9H1Y0） Autophagy-related protein 16-1 × 1 （Q676U5） SULFATE ION × 2 SODIUM ION × 1 water × 3 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 4 Ubiquitin-like protein ATG12 × 1 （O94817） Autophagy protein 5 × 1 （Q9H1Y0） Autophagy-related protein 16-1 × 1 （Q676U5） SULFATE ION × 4 SODIUM ION × 1 water × 4 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 4 Ubiquitin-like protein ATG12 × 1 （O94817） Autophagy protein 5 × 1 （Q9H1Y0） Autophagy-related protein 16-1 × 1 （Q676U5） SULFATE ION × 3 SODIUM ION × 1 water × 3 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
8fkm

1 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
4naw 4naw 4naw 4naw 9e8p 9e8p

6 assemblies

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.

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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. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

4naw__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4naw__assembly_1__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

4naw__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）23.55 Å
Rg (electron density)22.31 Å
Total Rg23.38 Å
Atom count6673
Residues401
Excluded volume59995 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 4naw__assembly_1__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 4naw__assembly_2__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 4naw__assembly_3__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 4naw__assembly_4__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (7)

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6. 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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7. Citations (1)