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Yorodumi- EMDB-20838: In situ structure of the export apparatus in Salmonella T3SS machine -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20838 | ||||||||||||
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Title | In situ structure of the export apparatus in Salmonella T3SS machine | ||||||||||||
Map data | Intact export apparatus in the Salmonella T3SS machine | ||||||||||||
Sample |
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Biological species | Salmonella enterica subsp. enterica serovar Abony (bacteria) | ||||||||||||
Method | subtomogram averaging / Resolution: 17.0 Å | ||||||||||||
Authors | Liu J | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2019 Title: High-resolution view of the type III secretion export apparatus in situ reveals membrane remodeling and a secretion pathway. Authors: Carmen Butan / Maria Lara-Tejero / Wenwei Li / Jun Liu / Jorge E Galán / Abstract: Type III protein secretion systems are essential virulence factors for many important pathogenic bacteria. The entire protein secretion machine is composed of several substructures that organize into ...Type III protein secretion systems are essential virulence factors for many important pathogenic bacteria. The entire protein secretion machine is composed of several substructures that organize into a holostructure or injectisome. The core component of the injectisome is the needle complex, which houses the export apparatus that serves as a gate for the passage of the secreted proteins through the bacterial inner membrane. Here, we describe a high-resolution structure of the export apparatus of the type III secretion system in association with the needle complex and the underlying bacterial membrane, both in isolation and in situ. We show the precise location of the core export apparatus components within the injectisome and bacterial envelope and demonstrate that their deployment results in major membrane remodeling and thinning, which may be central for the protein translocation process. We also show that InvA, a critical export apparatus component, forms a multiring cytoplasmic conduit that provides a pathway for the type III secretion substrates to reach the entrance of the export gate. Combined with structure-guided mutagenesis, our studies provide major insight into potential mechanisms of protein translocation and injectisome assembly. | ||||||||||||
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_20838.map.gz | 12.7 MB | EMDB map data format | |
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Header (meta data) | emd-20838-v30.xml emd-20838.xml | 9 KB 9 KB | Display Display | EMDB header |
Images | emd_20838.png | 83.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20838 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20838 | HTTPS FTP |
-Validation report
Summary document | emd_20838_validation.pdf.gz | 78.2 KB | Display | EMDB validaton report |
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Full document | emd_20838_full_validation.pdf.gz | 77.3 KB | Display | |
Data in XML | emd_20838_validation.xml.gz | 495 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20838 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20838 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_20838.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Intact export apparatus in the Salmonella T3SS machine | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.7 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 : Export Apparatus in type III secretion machine
Entire | Name: Export Apparatus in type III secretion machine |
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Components |
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-Supramolecule #1: Export Apparatus in type III secretion machine
Supramolecule | Name: Export Apparatus in type III secretion machine / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Salmonella enterica subsp. enterica serovar Abony (bacteria) |
-Experimental details
-Structure determination
Processing | subtomogram averaging |
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Aggregation state | cell |
-Sample preparation
Buffer | pH: 7 / Details: PBS |
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Grid | Model: Quantifoil R2/4 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 17.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Version: 0.09 / Number subtomograms used: 2000 |
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Extraction | Number tomograms: 1000 / Number images used: 3000 / Software - Name: IMOD |
CTF correction | Software - Name: IMOD |
Final angle assignment | Type: OTHER |