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Yorodumi- EMDB-11312: Structure of the Shigella MxiH needle filament attached to the ba... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11312 | |||||||||
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Title | Structure of the Shigella MxiH needle filament attached to the basal body | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Type 3 secretion system / Shigella / Helical reconstruction / Needle filament. / PROTEIN TRANSPORT | |||||||||
Function / homology | Function and homology information type III protein secretion system complex / protein secretion by the type III secretion system / cell surface / extracellular region / identical protein binding Similarity search - Function | |||||||||
Biological species | Shigella flexneri 5a str. M90T (bacteria) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Lunelli M / Kotov V | |||||||||
Funding support | Germany, 2 items
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Citation | Journal: Biochem Biophys Rep / Year: 2021 Title: Helical reconstruction of and needle filaments attached to type 3 basal bodies. Authors: Vadim Kotov / Michele Lunelli / Jiri Wald / Michael Kolbe / Thomas C Marlovits / Abstract: Gram-negative pathogens evolved a syringe-like nanomachine, termed type 3 secretion system, to deliver protein effectors into the cytoplasm of host cells. An essential component of this system is a ...Gram-negative pathogens evolved a syringe-like nanomachine, termed type 3 secretion system, to deliver protein effectors into the cytoplasm of host cells. An essential component of this system is a long helical needle filament that protrudes from the bacterial surface and connects the cytoplasms of the bacterium and the eukaryotic cell. Previous structural research was predominantly focused on reconstituted type 3 needle filaments, which lacked the biological context. In this work we introduce a facile procedure to obtain high-resolution cryo-EM structure of needle filaments attached to the basal body of type 3 secretion systems. We validate our approach by solving the structure of PrgI filament and demonstrate its utility by obtaining the first high-resolution cryo-EM reconstruction of Shigella MxiH filament. Our work paves the way to systematic structural characterization of attached type 3 needle filaments in the context of mutagenesis studies, protein structural evolution and drug development. | |||||||||
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_11312.map.gz | 5.1 MB | EMDB map data format | |
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Header (meta data) | emd-11312-v30.xml emd-11312.xml | 17.1 KB 17.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_11312_fsc.xml | 10.6 KB | Display | FSC data file |
Images | emd_11312.png | 138 KB | ||
Filedesc metadata | emd-11312.cif.gz | 5.7 KB | ||
Others | emd_11312_half_map_1.map.gz emd_11312_half_map_2.map.gz | 80.8 MB 81 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11312 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11312 | HTTPS FTP |
-Validation report
Summary document | emd_11312_validation.pdf.gz | 674.2 KB | Display | EMDB validaton report |
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Full document | emd_11312_full_validation.pdf.gz | 673.7 KB | Display | |
Data in XML | emd_11312_validation.xml.gz | 18.3 KB | Display | |
Data in CIF | emd_11312_validation.cif.gz | 23.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11312 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11312 | HTTPS FTP |
-Related structure data
Related structure data | 6zniMC 6znhC M: atomic model generated by this map 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_11312.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.38369 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: #2
File | emd_11312_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_11312_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Needle filament of the type III secretion system
Entire | Name: Needle filament of the type III secretion system |
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Components |
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-Supramolecule #1: Needle filament of the type III secretion system
Supramolecule | Name: Needle filament of the type III secretion system / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all Details: Structure obtained from needles attached to the basal body |
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Source (natural) | Organism: Shigella flexneri 5a str. M90T (bacteria) |
-Macromolecule #1: Protein MxiH
Macromolecule | Name: Protein MxiH / type: protein_or_peptide / ID: 1 / Number of copies: 23 / Enantiomer: LEVO |
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Source (natural) | Organism: Shigella flexneri 5a str. M90T (bacteria) |
Molecular weight | Theoretical: 11.060279 KDa |
Recombinant expression | Organism: Shigella flexneri 5a str. M90T (bacteria) |
Sequence | String: MASWSHPQFE KIEGRMSVTV PNDDWTLSSL SETFDDGTQT LQGELTLALD KLAKNPSNPQ LLAEYQSKLS EYTLYRNAQS NTVKVIKDV DAAIIQNFR UniProtKB: Type 3 secretion system needle filament protein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 0.5 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Frames/image: 1-6 / Number grids imaged: 1 / Number real images: 5238 / Average exposure time: 1.5 sec. / Average electron dose: 25.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 100000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |