SAXSdb — 6wy6

▼

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

Autophagy-related protein 8

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	EH domain-containing and endocytosis protein 1 × 1 （P34216） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	EH domain-containing and endocytosis protein 1 × 1 （P34216） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ATG8_YEAS7
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–118； UniProt 1–116 Author chain B； PDBConstruct 3–118； UniProt 1–116

EH domain-containing and endocytosis protein 1

OrganismNot specified

UniProt P34216

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Autophagy-related protein 8 × 1 （A6ZKM4） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Autophagy-related protein 8 × 1 （A6ZKM4） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	EDE1_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–28； UniProt 1220–1247 Author chain D； PDBConstruct 1–28； UniProt 1220–1247

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	6wy6
Deposition date deposition_date	2020-05-12
Structure title title	Crystal structure of S. cerevisiae Atg8 in complex with Ede1 (1220-1247)
Keywords keywords	;selective autophagy, clathrin-mediated endocytosis, intrinsic receptor, Atg8, Ede1, cryo-electron tomography, liquid-liquid phase separation, LLPS, PROTEIN TRANSPORT ;; PROTEIN TRANSPORT
Experimental Method method	X-RAY DIFFRACTION

▼

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.

6wy6__assembly_1__model_1

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

Download this curve (.dat)

6wy6__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6wy6__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	16.00 Å
Rg (electron density)	14.67 Å
Total Rg	15.83 Å
Atom count	1080
Residues	135
Excluded volume	19298 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6wy6__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6wy6__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Autophagy-related protein 8
Molecular weight formula_weight	13603.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,A
Atom count atom_count	2422

GSMKSTFKSEYPFEKRKAESERIADRFPNRIPVICEKAEKSDIPEIDKRKYLVPADLTVGQFVYVIRKRIMLPPEKAIFIFVNDTLPPTAALMSAIYQEHKDKDGFLYVTYSGENTFG

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

Entity 2 Entity 2 polymer

Description description	EH domain-containing and endocytosis protein 1
Molecular weight formula_weight	3172.3 kDa
Mutation mutation	D1247E
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

ADSESEFENVANAGSMEQFETIDHKDLN

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	216

▶

Unit-cell length a length_a	49.642 Å
Unit-cell length b length_b	49.642 Å
Unit-cell length c length_c	123.446 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 43
Space-group number int_tables_number	78
Crystal system crystal_system	—

Resolution resolution	1.773 Å
Low-resolution limit resolution_low	46.057 Å
R factor r_factor	0.1771
R_work r_work	0.1756
R_free r_free	0.2028

Crystal structure of S. cerevisiae Atg8 in complex with Ede1 (1220-1247)

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

Autophagy-related protein 8

State in the Current Structure

Other States of the Same Protein in the Database

EH domain-containing and endocytosis protein 1

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

6wy6__assembly_1__model_1

6wy6__assembly_1__model_1 | I(q)

6wy6__assembly_1__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

Entity 3 Entity 3 water

7. Citations (1)

Crystal structure of S. cerevisiae Atg8 in complex with Ede1 (1220-1247)

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

Autophagy-related protein 8

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

EH domain-containing and endocytosis protein 1

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

6wy6__assembly_1__model_1

6wy6__assembly_1__model_1 | I(q)

6wy6__assembly_1__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

Entity 3 Entity 3 water

7. Citations (1)