SAXSdb — 6aaf

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

Autophagy-related protein 8

Schizosaccharomyces pombe (strain 972 / ATCC 24843)

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–116	Not recorded	Transmembrane protein 184 homolog C30D11.06c × 1 （Q09906）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；27.5% PEG8000, 0.2 M sodium acetate, 0.1 M Bis-Tris pH 5.5	Resolution 2.20 Å R-free 0.259

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	ATG8_SCHPO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–119； UniProt 1–116

Transmembrane protein 184 homolog C30D11.06c

Schizosaccharomyces pombe (strain 972 / ATCC 24843)

UniProt Q09906

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 386–409	Not recorded	Autophagy-related protein 8 × 1 （O94272）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；27.5% PEG8000, 0.2 M sodium acetate, 0.1 M Bis-Tris pH 5.5	Resolution 2.20 Å R-free 0.259

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 6AAF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7YO8 Crystal structure of fission yeast Hfl1 LIR fused to human GABARAPL2 Deposited 2022-08-01	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 386–409（24 aa）	Mutation：F28S V29T	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.8；293 K；8% PEG 3000, 0.1 M sodium citrate	Resolution 1.80 Å R-free 0.205

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TM184_SCHPO
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–25； UniProt 386–409

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	6aaf
Deposition date deposition_date	2018-07-18
Structure title title	Crystal structure of fission yeast Atg8 complexed with the helical AIM of Hfl1.
Keywords keywords	vacuole, autophagy, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	15.90 Å
Radius of gyration Rg (electron density) rg_electron	14.37 Å
Forward intensity I(0) i0	4319730.00
Molecular weight molecular_weight	15373.0 kDa
Excluded volume excluded_volume	19528 Å³
Envelope volume envelope_volume	22210 Å³
Hydration-shell volume shell_volume	13103 Å³
Envelope diameter envelope_diameter	50.3 Å
Shell Rg shell_rg	20.20 Å
Envelope Rg envelope_rg	14.58 Å
Shape Rg shape_rg	14.37 Å
Total Rg total_rg	15.63 Å
Total atoms total_atoms	1085
Residues n_residues	134
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	50.3 Å
Rg (real space) rg_real	15.78 Å
Rg uncertainty (real space) rg_real_error	0.31 Å
I(0) (real space) i0_real	4.3200e+06
I(0) uncertainty (real space) i0_real_error	5.2120e+04
Rg (reciprocal space) rg_reciprocal	15.80 Å
I(0) (reciprocal space) i0_reciprocal	4320000.0000
Solution quality estimate total_estimate	0.8815
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.9 Å
Skewness Skewness skewness	0.082
Kurtosis Kurtosis kurtosis	-0.372
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	974900.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.826; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.988

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Autophagy-related protein 8
Molecular weight formula_weight	13876.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1089

GPHMRSQFKDDFSFEKRKTESQRIREKYPDRIPVICEKVDKSDIAAIDKKKYLVPSDLTVGQFVYVIRKRIKLSPEKAIFIFIDEILPPTAALMSTIYEEHKSEDGFLYITYSGENTFG

来源 Source

来源生物 organism	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
通用名 common_name	Fission yeast
NCBI Class编号 ncbi_taxonomy_id	284812
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Transmembrane protein 184 homolog C30D11.06c
Molecular weight formula_weight	3860.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MLQFEIDDEMEPLYNQAKQMRYGDYLEVLFQ

来源 Source

来源生物 organism	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
通用名 common_name	Fission yeast
NCBI Class编号 ncbi_taxonomy_id	284812
宿主生物 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	4

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d6aafa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.0 — automated matches

CATH v4.4 (1 domains)

Domain ID domain_id	6aafA00
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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8. Citations (1)

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Unit-cell length a length_a	33.798 Å
Unit-cell length b length_b	108.866 Å
Unit-cell length c length_c	35.120 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	4

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.197 Å
Low-resolution limit resolution_low	35.120 Å
R factor r_factor	0.2161
R_work r_work	0.2112
R_free r_free	0.2593

fit	/app/data/saxs_computation/aa/6aaf/6aaf.fit
pddf	/app/data/pr_computation/aa/6aaf/6aaf.pr.out
profile	/app/data/saxs_computation/aa/6aaf/6aaf.dat

Crystal structure of fission yeast Atg8 complexed with the helical AIM of Hfl1.

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

Transmembrane protein 184 homolog C30D11.06c

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)