SAXSdb — 6h3n

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

VgrG1

Pseudomonas aeruginosa PAO1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	No other associated polymer	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9I741_PSEAE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–643； UniProt 1–643 Author chain B； PDBConstruct 1–643； UniProt 1–643 Author chain C； PDBConstruct 1–643； UniProt 1–643

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	6h3n
Deposition date deposition_date	2018-07-19
Structure title title	Structure of VgrG1 in the Type VI secretion VgrG1-Tse6-EF-Tu complex embedded in lipid nanodiscs
Keywords keywords	Bacterial Type VI effector complex, Tse6-loaded VgrG1 complex, TOXIN; TOXIN
Experimental Method method	ELECTRON MICROSCOPY

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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.

6h3n__assembly_1__model_1

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

Download this curve (.dat)

6h3n__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6h3n__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	47.87 Å
Rg (electron density)	48.54 Å
Total Rg	48.60 Å
Atom count	29319
Residues	1881
Excluded volume	261240 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6h3n__assembly_1__model_1`	trimeric （3）	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 (1)

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6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	6h3nA01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	110 — Pnp Oxidase; Chain A
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	6h3nA02
Class class	3 — Alpha Beta
Architecture architecture	55 — 3-Layer(bab) Sandwich
Topology topology	50 — Phage tail protein beta-alpha-beta fold
Homologous superfamily homologous superfamily	10 — Baseplate protein-like domains

Domain ID domain_id	6h3nA03
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	220 — Light-harvesting Protein
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	6h3nA04
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	230 — Gp5 N-terminal domain

Domain ID domain_id	6h3nB01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	110 — Pnp Oxidase; Chain A
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	6h3nB02
Class class	3 — Alpha Beta
Architecture architecture	55 — 3-Layer(bab) Sandwich
Topology topology	50 — Phage tail protein beta-alpha-beta fold
Homologous superfamily homologous superfamily	10 — Baseplate protein-like domains

Domain ID domain_id	6h3nB03
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	220 — Light-harvesting Protein
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	6h3nB04
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	230 — Gp5 N-terminal domain

Domain ID domain_id	6h3nC01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	110 — Pnp Oxidase; Chain A
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	6h3nC02
Class class	3 — Alpha Beta
Architecture architecture	55 — 3-Layer(bab) Sandwich
Topology topology	50 — Phage tail protein beta-alpha-beta fold
Homologous superfamily homologous superfamily	10 — Baseplate protein-like domains

Domain ID domain_id	6h3nC03
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	220 — Light-harvesting Protein
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	6h3nC04
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	230 — Gp5 N-terminal domain

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

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

Resolution resolution	3.25 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	72000

Description description	VgrG1
Molecular weight formula_weight	72098.4 kDa
Source method src_method	man
Copy count entity_count	3

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	29319

Structure of VgrG1 in the Type VI secretion VgrG1-Tse6-EF-Tu complex embedded in lipid nanodiscs

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

VgrG1

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

6h3n__assembly_1__model_1

6h3n__assembly_1__model_1 | I(q)

6h3n__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)

Source organism organism	Pseudomonas aeruginosa PAO1
NCBI taxonomy ID ncbi_taxonomy_id	208964
Host organism host_organism	Escherichia coli BL21

Structure of VgrG1 in the Type VI secretion VgrG1-Tse6-EF-Tu complex embedded in lipid nanodiscs

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

VgrG1

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

6h3n__assembly_1__model_1

6h3n__assembly_1__model_1 | I(q)

6h3n__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)