SAXSdb — 3vx8

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

Ubiquitin-like modifier-activating enzyme atg7

Arabidopsis thaliana

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 3 × 1 （Q0WWQ1） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Autophagy-related protein 3 × 1 （Q0WWQ1） water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ATG7_ARATH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–323； UniProt 7–325 Author chain D； PDBConstruct 5–323； UniProt 7–325

Autophagy-related protein 3

Arabidopsis thaliana

UniProt Q0WWQ1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Ubiquitin-like modifier-activating enzyme atg7 × 1 （Q94CD5） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Ubiquitin-like modifier-activating enzyme atg7 × 1 （Q94CD5） water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ATG3_ARATH
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 5–292； UniProt 26–313 Author chain C； PDBConstruct 5–292； UniProt 26–313

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	3vx8
Deposition date deposition_date	2012-09-11
Structure title title	Crystal structure of Arabidopsis thaliana Atg7NTD-Atg3 complex
Keywords keywords	E1-E2 complex, Ligase; LIGASE
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.

3vx8__assembly_1__model_1

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

Download this curve (.dat)

3vx8__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3vx8__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.65 Å
Rg (electron density)	23.74 Å
Total Rg	24.79 Å
Atom count	3834
Residues	480
Excluded volume	68451 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3vx8__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3vx8__assembly_2__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	Ubiquitin-like modifier-activating enzyme atg7
Molecular weight formula_weight	36012.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,A
Atom count atom_count	7608

GPHMPAIILQFAPLNSSVDEGFWHSFSSLKLDKLGIDDSPISITGFYGPCGHPQVSNHLTLLSESLPLDEQSLIASTSHGNRNKCPVPGILYNTNTVESFNKLDKQSLLKAEANKIWEDIQSGKALEDPSVLPRFLVISFADLKKWSFRYWFAFPAFVLDPPVSLIELKPASEYFSSEEAESVSAACNDWRDSDLTTDVPFFLVSVSSDSKASIRHLKDLEACQGDHQKLLFGFYDPCHLPSNPGWPLRNYLALIRSRWNLETVWFFCYRESRGFADLNLSLVGQASITLSSGESAETVPNSVGWELNKGKRVPRSISLANSM

Source Source

Source organism organism	Arabidopsis thaliana
Common name common_name	mouse-ear cress
NCBI taxonomy ID ncbi_taxonomy_id	3702
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Autophagy-related protein 3
Molecular weight formula_weight	33010.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GPHMAFKEKGVLSVSEFVLAGDNLVSKCPTWSWESGDASKRKPYLPSDKQFLITRNVPCLRRAASVAEDYEAAGGEVLVDDEDNDGWLATHGKPKDKGKEEDNLPSMDALDINEKNTIQSIPTYFGGEEDDDIPDMEEFDEADNVVENDPATLQSTYLVAHEPDDDNILRTRTYDLSITYDKYYQTPRVWLTGYDESRMLLQPELVMEDVSQDHARKTVTIEDHPHLPGKHASVHPCRHGAVMKKIIDVLMSRGVEPEVDKYLFLFLKFMASVIPTIEYDYTMDFDLGSSST

Source Source

Source organism organism	Arabidopsis thaliana
Common name common_name	mouse-ear cress
NCBI taxonomy ID ncbi_taxonomy_id	3702
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	3

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3vx8A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	140 — Cytidine Deaminase; domain 2
Homologous superfamily homologous superfamily	100 — Ubiquitin-like modifier-activating enzyme ATG7 C-terminal domain

Domain ID domain_id	3vx8A02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	140 — Cytidine Deaminase; domain 2
Homologous superfamily homologous superfamily	70 — Ubiquitin-like modifier-activating enzyme ATG7 N-terminal domain

Domain ID domain_id	3vx8D01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	140 — Cytidine Deaminase; domain 2
Homologous superfamily homologous superfamily	100 — Ubiquitin-like modifier-activating enzyme ATG7 C-terminal domain

Domain ID domain_id	3vx8D02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	140 — Cytidine Deaminase; domain 2
Homologous superfamily homologous superfamily	70 — Ubiquitin-like modifier-activating enzyme ATG7 N-terminal domain

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Unit-cell length a length_a	101.520 Å
Unit-cell length b length_b	132.683 Å
Unit-cell length c length_c	102.805 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 2 2 21
Space-group number int_tables_number	17
Crystal system crystal_system	—

Resolution resolution	3.110 Å
Low-resolution limit resolution_low	34.850 Å
R factor r_factor	0.2287
R_work r_work	0.2261
R_free r_free	0.2777

Crystal structure of Arabidopsis thaliana Atg7NTD-Atg3 complex

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

Ubiquitin-like modifier-activating enzyme atg7

State in the Current Structure

Other States of the Same Protein in the Database

Autophagy-related protein 3

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

3vx8__assembly_1__model_1

3vx8__assembly_1__model_1 | I(q)

3vx8__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

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (2)

Crystal structure of Arabidopsis thaliana Atg7NTD-Atg3 complex

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

Ubiquitin-like modifier-activating enzyme atg7

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-related protein 3

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

3vx8__assembly_1__model_1

3vx8__assembly_1__model_1 | I(q)

3vx8__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

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (2)