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Yorodumi- EMDB-20611: In situ structure of Shigella flexneri type III secretion system -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20611 | |||||||||
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Title | In situ structure of Shigella flexneri type III secretion system | |||||||||
Map data | Shigella T3SS | |||||||||
Sample |
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Biological species | Shigella flexneri 5a str. M90T (bacteria) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 27.0 Å | |||||||||
Authors | Liu J / Chang YJ | |||||||||
Funding support | United States, 2 items
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Citation | Journal: J Biol Chem / Year: 2019 Title: The cytoplasmic domain of MxiG interacts with MxiK and directs assembly of the sorting platform in the type III secretion system. Authors: Shoichi Tachiyama / Yunjie Chang / Meenakumari Muthuramalingam / Bo Hu / Michael L Barta / Wendy L Picking / Jun Liu / William D Picking / Abstract: Many Gram-negative bacteria use type III secretion systems (T3SSs) to inject virulence effector proteins into eukaryotic cells. The T3SS apparatus (T3SA) is structurally conserved among diverse ...Many Gram-negative bacteria use type III secretion systems (T3SSs) to inject virulence effector proteins into eukaryotic cells. The T3SS apparatus (T3SA) is structurally conserved among diverse bacterial pathogens and consists of a cytoplasmic sorting platform, an envelope-spanning basal body, and an extracellular needle with tip complex. The sorting platform is essential for effector recognition and powering secretion. Studies using bacterial "minicells" have revealed an unprecedented level of structural detail of the sorting platform; however, many of the structure-function relationships within this complex remain enigmatic. Here, we report on improved cryo-electron tomographic approaches to enhance the resolution of the T3SA sorting platform (at ≤2 nm resolution) done in concert with biochemical and genetic methods to define the sorting platform interactome and interactions with the T3SA inner membrane ring (IR). We observed that the sorting platform consists of "pods" with 6-fold symmetry that interact with the Spa47 ATPase via radial extensions comprising MxiN. Most importantly, MxiK maintained an interaction with the IR via specific interactions with the cytoplasmic domain of the IR protein MxiG (MxiG), which is a noncanonical forkhead-associated domain, and MxiK has an elongated structure that interacts with the IR via MxiG T4 lysozyme-mediated insertional mutagenesis of MxiK revealed its orientation within the sorting platform and enabled disruption of interactions with its binding partners, which abolished sorting platform assembly. Finally, a comparison with the homologous interactions in the T3SS sorting platform revealed clear differences in their IR-sorting platform interfaces that have possible mechanistic implications. | |||||||||
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_20611.map.gz | 11.6 MB | EMDB map data format | |
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Header (meta data) | emd-20611-v30.xml emd-20611.xml | 8.4 KB 8.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_20611_fsc.xml | 5.7 KB | Display | FSC data file |
Images | emd_20611.png | 62.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20611 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20611 | HTTPS FTP |
-Validation report
Summary document | emd_20611_validation.pdf.gz | 78.8 KB | Display | EMDB validaton report |
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Full document | emd_20611_full_validation.pdf.gz | 77.8 KB | Display | |
Data in XML | emd_20611_validation.xml.gz | 496 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20611 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20611 | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_20611.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Shigella T3SS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 5.2 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 III secretion system of Shigella flexneri
Entire | Name: Type III secretion system of Shigella flexneri |
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Components |
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-Supramolecule #1: Type III secretion system of Shigella flexneri
Supramolecule | Name: Type III secretion system of Shigella flexneri / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Shigella flexneri 5a str. M90T (bacteria) / Strain: M90T |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.3 |
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Grid | Material: COPPER / Mesh: 200 |
Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / 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: Tecnai Polara / Image courtesy: FEI Company |