4mtk

Crystal structure of PA0091 VgrG1, the central spike of the Type VI Secretion System

Method: X-RAY DIFFRACTION

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

VgrG1

Pseudomonas aeruginosa

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	SULFATE ION × 143 TRIS(HYDROXYETHYL)AMINOMETHANE × 1 water × 3	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 3	SULFATE ION × 113 TRIS(HYDROXYETHYL)AMINOMETHANE × 1 water × 3	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 Author chain D； PDBConstruct 1–643； UniProt 1–643 Author chain E； PDBConstruct 1–643； UniProt 1–643 Author chain F； 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	4mtk
Deposition date deposition_date	2013-09-19
Structure title title	Crystal structure of PA0091 VgrG1, the central spike of the Type VI Secretion System
Keywords keywords	Beta-barrel, OB-fold, Beta-helix, Type VI secretion system central spike, Secreted outside of the cell, TOXIN; TOXIN
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.

4mtk__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4mtk__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4mtk__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	47.34 Å
Rg (electron density)	48.16 Å
Total Rg	48.14 Å
Atom count	15507
Residues	1881
Excluded volume	267870 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4mtk__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4mtk__assembly_2__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 (4)

Entity 1 Entity 1 polymer

Description description	VgrG1
Molecular weight formula_weight	72098.4 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	31170

MQLTRLVQVDCPLGPDVLLLQRMEGREELGRLFAYELHLVSENPNLPLEQLLGKPMSLSLELPGGSRRFFHGIVARCSQVAGHGQFAGYQATLRPWPWLLTRTSDCRIFQNQSVPEIIKQVFRNLGFSDFEDALTRPYREWEYCVQYRETSFDFISRLMEQEGIYYWFRHEQKRHILVLSDAYGAHRSPGGYASVPYYPPTLGHRERDHFFDWQMAREVQPGSLTLNDYDFQRPGARLEVRSNIARPHAAADYPLYDYPGEYVQSQDGEQYARNRIEAIQAQHERVRLRGVVRGIGAGHLFRLSGYPRDDQNREYLVVGAEYRVVQELYETGSGGAGSQFESELDCIDASQSFRLLPQTPVPVVRGPQTAVVVGPKGEEIWTDQYGRVKVHFHWDRHDQSNENSSCWIRVSQAWAGKNWGSMQIPRIGQEVIVSFLEGDPDRPIITGRVYNAEQTVPYELPANATQSGMKSRSSKGGTPANFNEIRMEDKKGAEQLYIHAERNQDNLVENDASLSVGHDRNKSIGHDELARIGNNRTRAVKLNDTLLVGGAKSDSVTGTYLIEAGAQIRLVCGKSVVEFNADGTINISGSAFNLYASGNGNIDTGGRLDLNSGGASEVDAKGKGVQGTIDGQVQAMFPPPAKG

Source Source

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

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	256

Entity 3 Entity 3 non-polymer

Description description	TRIS(HYDROXYETHYL)AMINOMETHANE
Molecular weight formula_weight	163.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	6

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6. Fold Classification (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

Domain ID domain_id	4mtkA01
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	4mtkA02
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	4mtkA03
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	4mtkA04
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	4mtkB01
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	4mtkB02
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	4mtkB03
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	4mtkB04
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	4mtkC01
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	4mtkC02
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	4mtkC03
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	4mtkC04
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	4mtkD01
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	4mtkD02
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	4mtkD03
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	4mtkD04
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	4mtkE01
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	4mtkE02
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	4mtkE03
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	4mtkE04
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	4mtkF01
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	4mtkF02
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	4mtkF03
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	4mtkF04
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	168.275 Å
Unit-cell length b length_b	168.275 Å
Unit-cell length c length_c	652.849 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	36

Space group space_group	P 61
Space-group number int_tables_number	169
Crystal system crystal_system	—

Resolution resolution	3.322 Å
Low-resolution limit resolution_low	49.143 Å
R factor r_factor	0.1754
R_work r_work	0.1697
R_free r_free	0.1954

Crystal structure of PA0091 VgrG1, the central spike of the Type VI Secretion System

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

4mtk__assembly_2__model_1

4mtk__assembly_2__model_1 | I(q)

4mtk__assembly_2__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

7. Citations (1)

Crystal structure of PA0091 VgrG1, the central spike of the Type VI Secretion System

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

4mtk__assembly_2__model_1

4mtk__assembly_2__model_1 | I(q)

4mtk__assembly_2__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

7. Citations (1)