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Yorodumi- EMDB-3113: Negative stain EM structure of the Tse6-Tsi6-VgrG1-EagT6-EF-Tu complex -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3113 | |||||||||
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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 |
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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 / guanosine tetraphosphate binding / translational elongation ...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 / guanosine tetraphosphate binding / translational elongation / translation elongation factor activity / response to antibiotic / GTPase activity / GTP binding / RNA binding / extracellular region / membrane / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Pseudomonas aeruginosa PAO1 (bacteria) / Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 21.5 Å | |||||||||
Authors | Whitney J / Quentin D / Sawai S / LeRoux M / Harding B / Ledvina H / Tran B / Robinson H / Goo YA / Goodlett D ...Whitney J / Quentin D / Sawai S / LeRoux M / Harding B / Ledvina H / Tran B / Robinson H / Goo YA / Goodlett D / Raunser S / Mougous J | |||||||||
Citation | 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_3113.map.gz | 5 MB | EMDB map data format | |
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Header (meta data) | emd-3113-v30.xml emd-3113.xml | 12.6 KB 12.6 KB | Display Display | EMDB header |
Images | emd_3113.tif | 50.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3113 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3113 | HTTPS FTP |
-Validation report
Summary document | emd_3113_validation.pdf.gz | 182.4 KB | Display | EMDB validaton report |
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Full document | emd_3113_full_validation.pdf.gz | 181.6 KB | Display | |
Data in XML | emd_3113_validation.xml.gz | 5.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3113 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3113 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_3113.map.gz / Format: CCP4 / Size: 5.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of Tse6-Tsi6-VgrG1-EagT6-EF-Tu complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.64 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Tse6-Tsi6-VgrG1-EagT6-EF-Tu complex
Entire | Name: Tse6-Tsi6-VgrG1-EagT6-EF-Tu complex |
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Components |
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-Supramolecule #1000: Tse6-Tsi6-VgrG1-EagT6-EF-Tu complex
Supramolecule | 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 |
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Molecular weight | Theoretical: 364 KDa |
-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 |
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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 |
-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 |
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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 |
-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 |
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Source (natural) | Organism: Pseudomonas aeruginosa PAO1 (bacteria) |
Molecular weight | Theoretical: 11 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | UniProtKB: Immune protein Tsi6 |
-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 |
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Source (natural) | Organism: Pseudomonas aeruginosa PAO1 (bacteria) |
Molecular weight | Theoretical: 16 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | UniProtKB: Effector EagT6 |
-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 |
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Source (natural) | Organism: Escherichia coli (E. coli) / synonym: Escherichia coli |
Molecular weight | Theoretical: 43 KDa |
Sequence | UniProtKB: Elongation factor Tu 1 |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.02 mg/mL |
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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 |
-Electron microscopy
Microscope | JEOL 1400 |
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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 |
Electron optics | Calibrated magnification: 67210 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 3.4 mm / Nominal defocus max: 0.002 µm / Nominal defocus min: 0.0012 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC |
-Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 21.5 Å / Resolution method: OTHER / Software - Name: SPARX / Number images used: 6863 |
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