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Yorodumi- EMDB-2481: Injectisome (wild type) from Salmonella typhimurium (substrate free) -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2481 | |||||||||
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Title | Injectisome (wild type) from Salmonella typhimurium (substrate free) | |||||||||
Map data | Reconstruction of substrate free needle complexes of the type-3 secretion system from Salmonella typhimurium | |||||||||
Sample |
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Keywords | Injectisome / Pathogenic Type-3 Secretion System / Protein delivery machine / Salmonella typhimurium | |||||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 10.0 Å | |||||||||
Authors | Radics J / Konigsmaier L / Marlovits TC | |||||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2014 Title: Structure of a pathogenic type 3 secretion system in action. Authors: Julia Radics / Lisa Königsmaier / Thomas C Marlovits / Abstract: Type 3 secretion systems use 3.5-megadalton syringe-like, membrane-embedded 'injectisomes', each containing an ~800-Å-long needle complex to connect intracellular compartments of infectious bacteria ...Type 3 secretion systems use 3.5-megadalton syringe-like, membrane-embedded 'injectisomes', each containing an ~800-Å-long needle complex to connect intracellular compartments of infectious bacteria and hosts. Here we identify requirements for substrate association with, transport through and exit from the injectisome of Salmonella enterica serovar Typhimurium. This guided the design of substrates that become trapped within the secretion path and enabled visualization of injectisomes in action in situ. We used cryo-EM to define the secretion path, providing a structural explanation as to why effector proteins must be unfolded during transport. Furthermore, trapping of a heterologous substrate in the needle prevents secretion of natural bacterial effectors. Together, the data reveal the path of protein secretion across multiple membranes and show that mechanisms rejecting unacceptable substrates can be undermined, and transport of bacterial effectors across an already assembled type 3 secretion system can be inhibited. | |||||||||
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_2481.map.gz | 95.9 MB | EMDB map data format | |
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Header (meta data) | emd-2481-v30.xml emd-2481.xml | 9.4 KB 9.4 KB | Display Display | EMDB header |
Images | emd_2481.tif | 760.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2481 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2481 | HTTPS FTP |
-Validation report
Summary document | emd_2481_validation.pdf.gz | 239.2 KB | Display | EMDB validaton report |
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Full document | emd_2481_full_validation.pdf.gz | 238.3 KB | Display | |
Data in XML | emd_2481_validation.xml.gz | 7.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2481 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2481 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_2481.map.gz / Format: CCP4 / Size: 100.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of substrate free needle complexes of the type-3 secretion system from Salmonella typhimurium | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.33 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 : Needle complex of the type-3 secretion system from Salmonella typ...
Entire | Name: Needle complex of the type-3 secretion system from Salmonella typhimurium |
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Components |
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-Supramolecule #1000: Needle complex of the type-3 secretion system from Salmonella typ...
Supramolecule | Name: Needle complex of the type-3 secretion system from Salmonella typhimurium type: sample / ID: 1000 / Details: The sample was mono disperse / Oligomeric state: 1 / Number unique components: 1 |
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Molecular weight | Theoretical: 3.5 MDa |
-Supramolecule #1: type 3 secretion system
Supramolecule | Name: type 3 secretion system / type: organelle_or_cellular_component / ID: 1 / Name.synonym: injectisome / Recombinant expression: No |
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Source (natural) | Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) Strain: SB905 / Location in cell: Plasma membrane |
Molecular weight | Theoretical: 3.5 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.05 mg/mL |
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Buffer | pH: 8 Details: 10 mM Tris, 500 mM NaCl, 5 mM EDTA, 0.1% (w/v) LDAO (n-Dodecyl-N,N-Dimethylamine-N-Oxide) |
Grid | Details: 400 mesh Mo-Grid with carbon support |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 60 % / Instrument: LEICA EM GP Method: 1. glow discharge 40sec/20mAmp 2. sample (5ul), 2min settling time 3. blotting 0.8-1.2sec |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Temperature | Min: 83 K / Max: 108 K / Average: 93 K |
Alignment procedure | Legacy - Astigmatism: objective lens astigmatism was corrected at appr 200.000 magnification |
Date | Feb 27, 2012 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Sampling interval: 15 µm / Average electron dose: 25 e/Å2 / Details: Image acquisition using LEGINON |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 112969 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 6.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 93000 |
Sample stage | Specimen holder: liquid nitrogen cooled / Specimen holder model: GATAN HELIUM |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
Details | reconstruction in C1, and then C3 symmetry imposed on C1-map |
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CTF correction | Details: ctf flip (CTFFIND3/images) |
Final reconstruction | Applied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 10.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: XMIPP, IMAGIC / Number images used: 74964 |
Final two d classification | Number classes: 2000 |