2dym

The crystal structure of Saccharomyces cerevisiae Atg5- Atg16(1-46) complex

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Autophagy protein 5

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Autophagy protein 16 × 1 （Q03818） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Autophagy protein 16 × 1 （Q03818） water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Autophagy protein 16 × 1 （Q03818） water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Autophagy protein 16 × 1 （Q03818） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ATG5_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–297； UniProt 1–294 Author chain C； PDBConstruct 4–297； UniProt 1–294 Author chain E； PDBConstruct 4–297； UniProt 1–294 Author chain G； PDBConstruct 4–297； UniProt 1–294

Autophagy protein 16

Saccharomyces cerevisiae

UniProt Q03818

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Autophagy protein 5 × 1 （Q12380） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Autophagy protein 5 × 1 （Q12380） water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Autophagy protein 5 × 1 （Q12380） water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Autophagy protein 5 × 1 （Q12380） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ATG16_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–46； UniProt 1–46 Author chain D； PDBConstruct 1–46； UniProt 1–46 Author chain F； PDBConstruct 1–46； UniProt 1–46 Author chain H； PDBConstruct 1–46； UniProt 1–46

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_id	2dym
Deposition date deposition_date	2006-09-15
Structure title title	The crystal structure of Saccharomyces cerevisiae Atg5- Atg16(1-46) complex
Keywords keywords	ubiquitin-fold, herix-bundle, PROTEIN TURNOVER-PROTEIN TURNOVER COMPLEX; PROTEIN TURNOVER/PROTEIN TURNOVER
Experimental Method method	X-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.

2dym__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2dym__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2dym__assembly_4__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	20.18 Å
Rg (electron density)	18.91 Å
Total Rg	20.02 Å
Atom count	2267
Residues	286
Excluded volume	40790 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2dym__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2dym__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2dym__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2dym__assembly_4__model_1`	dimeric （2）	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 (3)

Entity 1 Entity 1 polymer

Description description	Autophagy protein 5
Molecular weight formula_weight	33862.1 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G
Atom count atom_count	9196

GAHMNDIKQLLWNGELNVLVSIDPSFLMKGSPREIAVLRIRVPRETYLVNYMPLIWNKIKSFLSFDPLTDSEKYFWFEHNKTPIPWNYPVGVLFDCLAGKSATFTTSFENQVKDVLTFLRIHLVMGDSLPPTIIPIASSKTQAEKFWFHQWKQVCFILNGSSKAIMSLSVNEARKFWGSVITRNFQDFIEISNKISSSRPRHIPLIIQTSRTSGTFRISQPTISMTGVNPTLKDIEGDILDVKEGINGNDVMVICQGIEIPWHMLLYDLYSKLRSFDGFLYITLVPIKGGDKASSEL

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Autophagy protein 16
Molecular weight formula_weight	5500.2 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,H

MGNFIITERKKAKEERSNPQTDSMDDLLIRRLTDRNDKEAHLNELF

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	321

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6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	2dymA01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	620 —

Domain ID domain_id	2dymA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily	190 — Autophagy protein Apg5, helix rich domain

Domain ID domain_id	2dymA03
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	2dymC01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	620 —

Domain ID domain_id	2dymC02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily	190 — Autophagy protein Apg5, helix rich domain

Domain ID domain_id	2dymC03
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	2dymE01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	620 —

Domain ID domain_id	2dymE02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily	190 — Autophagy protein Apg5, helix rich domain

Domain ID domain_id	2dymE03
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	2dymG01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	620 —

Domain ID domain_id	2dymG02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily	190 — Autophagy protein Apg5, helix rich domain

Domain ID domain_id	2dymG03
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

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Unit-cell length a length_a	66.347 Å
Unit-cell length b length_b	104.417 Å
Unit-cell length c length_c	112.153 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.11 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	49.380 Å
R factor r_factor	0.2190
R_work r_work	0.2190
R_free r_free	0.2500

The crystal structure of Saccharomyces cerevisiae Atg5- Atg16(1-46) complex

1. Protein Identity and Related Structures Protein Identity & Related Structures

Autophagy protein 5

State in the Current Structure

Other States of the Same Protein in the Database

Autophagy protein 16

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2dym__assembly_4__model_1

2dym__assembly_4__model_1 | I(q)

2dym__assembly_4__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (2)

The crystal structure of Saccharomyces cerevisiae Atg5- Atg16(1-46) complex

1. Protein Identity and Related Structures Protein Identity & Related Structures

Autophagy protein 5

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Autophagy protein 16

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2dym__assembly_4__model_1

2dym__assembly_4__model_1 | I(q)

2dym__assembly_4__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (2)