- EMDB-3113: Negative stain EM structure of the Tse6-Tsi6-VgrG1-EagT6-EF-Tu complex -
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Basic information
Entry
Database: EMDB / ID: EMD-3113
Title
Negative stain EM structure of the Tse6-Tsi6-VgrG1-EagT6-EF-Tu complex
Map data
Reconstruction of Tse6-Tsi6-VgrG1-EagT6-EF-Tu complex
Sample
Sample: Tse6-Tsi6-VgrG1-EagT6-EF-Tu complex
Protein or peptide: Valine-glycine repeat protein 1
Protein or peptide: Type VI secretion exported 6
Protein or peptide: Type VI secretion immunity 6
Protein or peptide: Effector associated gene with tse6
Protein or peptide: Elongation factor Tu 1
Keywords
Type VI secretion system / bacterial competition / polymicrobial / effector / glycohydrolase
Function / homology
Function and homology information
type VI protein secretion system complex / protein secretion by the type VI secretion system / NAD+ glycohydrolase / toxin sequestering activity / NADP+ nucleosidase activity / guanyl-nucleotide exchange factor complex / NAD+ nucleosidase activity / NAD+ nucleotidase, cyclic ADP-ribose generating / translational elongation / guanosine tetraphosphate binding ...type VI protein secretion system complex / protein secretion by the type VI secretion system / NAD+ glycohydrolase / toxin sequestering activity / NADP+ nucleosidase activity / guanyl-nucleotide exchange factor complex / NAD+ nucleosidase activity / NAD+ nucleotidase, cyclic ADP-ribose generating / translational elongation / guanosine tetraphosphate binding / translation elongation factor activity / response to antibiotic / GTPase activity / GTP binding / RNA binding / extracellular region / membrane / plasma membrane / cytoplasm / cytosol Similarity search - Function
Tsi6 / Tsi6 / Inner membrane lipoprotein DcrB/EagT6 / Bacterial toxin 46 / DcrB / Bacterial toxin 46 / Mog1/PsbP, alpha/beta/alpha sandwich / PAAR motif / Type VI secretion system, RhsGE-associated Vgr family subset / PAAR motif ...Tsi6 / Tsi6 / Inner membrane lipoprotein DcrB/EagT6 / Bacterial toxin 46 / DcrB / Bacterial toxin 46 / Mog1/PsbP, alpha/beta/alpha sandwich / PAAR motif / Type VI secretion system, RhsGE-associated Vgr family subset / PAAR motif / Phage tail baseplate hub (GPD) / Type VI secretion system, RhsGE-associated Vgr protein / Gp5/Type VI secretion system Vgr protein, OB-fold domain / Type VI secretion system/phage-baseplate injector OB domain / Vgr protein, OB-fold domain superfamily / Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / P-loop containing nucleoside triphosphate hydrolase Similarity search - Domain/homology
Elongation factor Tu 1 / Effector EagT6 / NAD(P)(+) glycohydrolase toxin Tse6 / Immune protein Tsi6 / Type VI secretion system spike protein VgrG1a Similarity search - Component
Biological species
Pseudomonas aeruginosa PAO1 (bacteria) / Escherichia coli (E. coli)
Method
single particle reconstruction / negative staining / Resolution: 21.5 Å
Journal: Cell / Year: 2015 Title: An interbacterial NAD(P)(+) glycohydrolase toxin requires elongation factor Tu for delivery to target cells. Authors: John C Whitney / Dennis Quentin / Shin Sawai / Michele LeRoux / Brittany N Harding / Hannah E Ledvina / Bao Q Tran / Howard Robinson / Young Ah Goo / David R Goodlett / Stefan Raunser / Joseph D Mougous / Abstract: Type VI secretion (T6S) influences the composition of microbial communities by catalyzing the delivery of toxins between adjacent bacterial cells. Here, we demonstrate that a T6S integral membrane ...Type VI secretion (T6S) influences the composition of microbial communities by catalyzing the delivery of toxins between adjacent bacterial cells. Here, we demonstrate that a T6S integral membrane toxin from Pseudomonas aeruginosa, Tse6, acts on target cells by degrading the universally essential dinucleotides NAD(+) and NADP(+). Structural analyses of Tse6 show that it resembles mono-ADP-ribosyltransferase proteins, such as diphtheria toxin, with the exception of a unique loop that both excludes proteinaceous ADP-ribose acceptors and contributes to hydrolysis. We find that entry of Tse6 into target cells requires its binding to an essential housekeeping protein, translation elongation factor Tu (EF-Tu). These proteins participate in a larger assembly that additionally directs toxin export and provides chaperone activity. Visualization of this complex by electron microscopy defines the architecture of a toxin-loaded T6S apparatus and provides mechanistic insight into intercellular membrane protein delivery between bacteria.
History
Deposition
Aug 6, 2015
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Header (metadata) release
Aug 26, 2015
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Map release
Oct 21, 2015
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Update
Nov 25, 2015
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Current status
Nov 25, 2015
Processing site: PDBe / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Name: Tse6-Tsi6-VgrG1-EagT6-EF-Tu complex / type: sample / ID: 1000 Oligomeric state: Trimer of VgrG1 binds to monomers of Tse6, Tsi6, EF-Tu and a dimer of EagT6 Number unique components: 5
Molecular weight
Theoretical: 364 KDa
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Macromolecule #1: Valine-glycine repeat protein 1
Macromolecule
Name: Valine-glycine repeat protein 1 / type: protein_or_peptide / ID: 1 / Name.synonym: VgrG1 / Number of copies: 3 / Oligomeric state: Trimer / Recombinant expression: Yes
Source (natural)
Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weight
Theoretical: 72 KDa
Recombinant expression
Organism: Escherichia coli (E. coli)
Sequence
UniProtKB: Type VI secretion system spike protein VgrG1a
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Macromolecule #2: Type VI secretion exported 6
Macromolecule
Name: Type VI secretion exported 6 / type: protein_or_peptide / ID: 2 / Name.synonym: Tse6 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)
Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weight
Theoretical: 45 KDa
Recombinant expression
Organism: Escherichia coli (E. coli)
Sequence
UniProtKB: NAD(P)(+) glycohydrolase toxin Tse6
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Macromolecule #3: Type VI secretion immunity 6
Macromolecule
Name: Type VI secretion immunity 6 / type: protein_or_peptide / ID: 3 / Name.synonym: Tsi6 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)
Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weight
Theoretical: 11 KDa
Recombinant expression
Organism: Escherichia coli (E. coli)
Sequence
UniProtKB: Immune protein Tsi6
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Macromolecule #4: Effector associated gene with tse6
Macromolecule
Name: Effector associated gene with tse6 / type: protein_or_peptide / ID: 4 / Name.synonym: EagT6 / Number of copies: 2 / Oligomeric state: Dimer / Recombinant expression: Yes
Source (natural)
Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weight
Theoretical: 16 KDa
Recombinant expression
Organism: Escherichia coli (E. coli)
Sequence
UniProtKB: Effector EagT6
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Macromolecule #5: Elongation factor Tu 1
Macromolecule
Name: Elongation factor Tu 1 / type: protein_or_peptide / ID: 5 / Name.synonym: EF-Tu / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: No
Source (natural)
Organism: Escherichia coli (E. coli) / synonym: Escherichia coli
Molecular weight
Theoretical: 43 KDa
Sequence
UniProtKB: Elongation factor Tu 1
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Experimental details
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Structure determination
Method
negative staining
Processing
single particle reconstruction
Aggregation state
particle
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Sample preparation
Concentration
0.02 mg/mL
Buffer
pH: 8 / Details: 150 mM NaCl, 20 mM Tris-HCl
Staining
Type: NEGATIVE Details: Grids with adsorbed Protein floated on 0.75% Uranyl Formate for 45 sec
Grid
Details: glow discharged 400 mesh copper grids with thin carbon support
Vitrification
Cryogen name: NONE / Instrument: OTHER
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Electron microscopy
Microscope
JEOL 1400
Date
May 8, 2015
Image recording
Category: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Number real images: 200 / Average electron dose: 10 e/Å2
Electron beam
Acceleration voltage: 120 kV / Electron source: LAB6
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