+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3585 | |||||||||
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Title | Structure of the VirD4 bound to a Type IV secretion systemSecretion | |||||||||
Map data | Negative stain electron microscopy of the T4SS3-10 D4 complex enableslocalization of the VirD4 coupling protein within the complex. | |||||||||
Sample |
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Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 28.0 Å | |||||||||
Authors | Redzej A / Ukleja M | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: EMBO J / Year: 2017 Title: Structure of a VirD4 coupling protein bound to a VirB type IV secretion machinery. Authors: Adam Redzej / Marta Ukleja / Sarah Connery / Martina Trokter / Catarina Felisberto-Rodrigues / Adam Cryar / Konstantinos Thalassinos / Richard D Hayward / Elena V Orlova / Gabriel Waksman / Abstract: Type IV secretion (T4S) systems are versatile bacterial secretion systems mediating transport of protein and/or DNA T4S systems are generally composed of 11 VirB proteins and 1 VirD protein (VirD4). ...Type IV secretion (T4S) systems are versatile bacterial secretion systems mediating transport of protein and/or DNA T4S systems are generally composed of 11 VirB proteins and 1 VirD protein (VirD4). The VirB1-11 proteins assemble to form a secretion machinery and a pilus while the VirD4 protein is responsible for substrate recruitment. The structure of VirD4 in isolation is known; however, its structure bound to the VirB1-11 apparatus has not been determined. Here, we purify a T4S system with VirD4 bound, define the biochemical requirements for complex formation and describe the protein-protein interaction network in which VirD4 is involved. We also solve the structure of this complex by negative stain electron microscopy, demonstrating that two copies of VirD4 dimers locate on both sides of the apparatus, in between the VirB4 ATPases. Given the central role of VirD4 in type IV secretion, our study provides mechanistic insights on a process that mediates the dangerous spread of antibiotic resistance genes among bacterial populations. | |||||||||
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_3585.map.gz | 12.8 MB | EMDB map data format | |
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Header (meta data) | emd-3585-v30.xml emd-3585.xml | 11.7 KB 11.7 KB | Display Display | EMDB header |
Images | emd_3585.png | 226.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3585 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3585 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_3585.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Negative stain electron microscopy of the T4SS3-10 D4 complex enableslocalization of the VirD4 coupling protein within the complex. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.54 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 : Type IV secretion system, inner membrane complex
Entire | Name: Type IV secretion system, inner membrane complexSecretion |
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Components |
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-Supramolecule #1: Type IV secretion system, inner membrane complex
Supramolecule | Name: Type IV secretion system, inner membrane complex / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant strain: TOP10 / Recombinant plasmid: pR388 |
Molecular weight | Theoretical: 1.5 MDa |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.03 mg/mL |
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Buffer | pH: 7.6 Details: 50mM HEPES pH=7.6, 200mM sodium acetate, 0.1% digitonin, 0.05mM TDAO |
Staining | Type: NEGATIVE / Material: 2 % uranyl acetate / Details: Staining for 3 min |
Grid | Model: type B 400, Agar Scientific / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 4.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 41500 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm |
Image recording | Film or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Detector mode: INTEGRATING / Digitization - Frames/image: 2-19 / Average exposure time: 2.5 sec. / Average electron dose: 30.0 e/Å2 |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 14918 |
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CTF correction | Software - Name: CTFFIND (ver. 3) |
Startup model | Type of model: EMDB MAP EMDB ID: |
Initial angle assignment | Type: ANGULAR RECONSTITUTION / Software - Name: IMAGIC (ver. 5) |
Final 3D classification | Number classes: 2000 / Avg.num./class: 8 / Software - Name: IMAGIC (ver. 5) |
Final angle assignment | Type: ANGULAR RECONSTITUTION / Software - Name: IMAGIC (ver. 5) |
Final reconstruction | Number classes used: 700 / Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 28.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMAGIC (ver. 5) / Number images used: 2800 |