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Yorodumi- EMDB-3725: Negative-stain EM structure of the A. tumefaciens outer-membrane ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3725 | |||||||||
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Title | Negative-stain EM structure of the A. tumefaciens outer-membrane core complex | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Agrobacterium tumefaciens (bacteria) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 21.0 Å | |||||||||
Authors | Costa TRD / Orlova EV / Waksman G | |||||||||
Citation | Journal: Mol Microbiol / Year: 2017 Title: Use of chimeric type IV secretion systems to define contributions of outer membrane subassemblies for contact-dependent translocation. Authors: Jay E Gordon / Tiago R D Costa / Roosheel S Patel / Christian Gonzalez-Rivera / Mayukh K Sarkar / Elena V Orlova / Gabriel Waksman / Peter J Christie / Abstract: Recent studies have shown that conjugation systems of Gram-negative bacteria are composed of distinct inner and outer membrane core complexes (IMCs and OMCCs, respectively). Here, we characterized ...Recent studies have shown that conjugation systems of Gram-negative bacteria are composed of distinct inner and outer membrane core complexes (IMCs and OMCCs, respectively). Here, we characterized the OMCC by focusing first on a cap domain that forms a channel across the outer membrane. Strikingly, the OMCC caps of the Escherichia coli pKM101 Tra and Agrobacterium tumefaciens VirB/VirD4 systems are completely dispensable for substrate transfer, but required for formation of conjugative pili. The pKM101 OMCC cap and extended pilus also are dispensable for activation of a Pseudomonas aeruginosa type VI secretion system (T6SS). Chimeric conjugation systems composed of the IMC joined to OMCCs from the A. tumefaciens VirB/VirD4, E. coli R388 Trw, and Bordetella pertussis Ptl systems support conjugative DNA transfer in E. coli and trigger P. aeruginosa T6SS killing, but not pilus production. The A. tumefaciens VirB/VirD4 OMCC, solved by transmission electron microscopy, adopts a cage structure similar to the pKM101 OMCC. The findings establish that OMCCs are highly structurally and functionally conserved - but also intrinsically conformationally flexible - scaffolds for translocation channels. Furthermore, the OMCC cap and a pilus tip protein coregulate pilus extension but are not required for channel assembly or function. | |||||||||
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_3725.map.gz | 378.7 KB | EMDB map data format | |
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Header (meta data) | emd-3725-v30.xml emd-3725.xml | 7.7 KB 7.7 KB | Display Display | EMDB header |
Images | emd_3725.png | 116.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3725 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3725 | HTTPS FTP |
-Validation report
Summary document | emd_3725_validation.pdf.gz | 204.2 KB | Display | EMDB validaton report |
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Full document | emd_3725_full_validation.pdf.gz | 203.4 KB | Display | |
Data in XML | emd_3725_validation.xml.gz | 5.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3725 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3725 | 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_3725.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 3.3 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 outer-membrane core complex from A. tumefaciens
Entire | Name: Type IV secretion outer-membrane core complex from A. tumefaciens |
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Components |
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-Supramolecule #1: Type IV secretion outer-membrane core complex from A. tumefaciens
Supramolecule | Name: Type IV secretion outer-membrane core complex from A. tumefaciens type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Agrobacterium tumefaciens (bacteria) |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Staining | Type: NEGATIVE / Material: Uranyl Acetate |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Image recording | Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 21.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 1746 |
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Initial angle assignment | Type: ANGULAR RECONSTITUTION / Software - Name: IMAGIC |
Final angle assignment | Type: ANGULAR RECONSTITUTION / Software - Name: IMAGIC |