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Yorodumi- EMDB-8401: Single particle cryo-EM reconstruction of the Salmonella SPI-1 ty... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8401 | |||||||||
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Title | Single particle cryo-EM reconstruction of the Salmonella SPI-1 type III secretion injectisome secretin InvG at 4.4 Angstrom resolution | |||||||||
Map data | Single particle cryo-EM reconstruction of the Salmonella SPI-1 type III secretion injectisome secretin InvG at 4.4 Angstrom resolution | |||||||||
Sample |
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Function / homology | Function and homology information type III protein secretion system complex / type II protein secretion system complex / protein secretion by the type III secretion system / protein secretion / cell outer membrane / identical protein binding Similarity search - Function | |||||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.4 Å | |||||||||
Authors | Worrall LJ / Hong C / Vuckovic M / Bergeron JRC / Huang RK / Yu Z / Strynadka NCJ | |||||||||
Citation | Journal: Nature / Year: 2016 Title: Near-atomic-resolution cryo-EM analysis of the Salmonella T3S injectisome basal body. Authors: L J Worrall / C Hong / M Vuckovic / W Deng / J R C Bergeron / D D Majewski / R K Huang / T Spreter / B B Finlay / Z Yu / N C J Strynadka / Abstract: The type III secretion (T3S) injectisome is a specialized protein nanomachine that is critical for the pathogenicity of many Gram-negative bacteria, including purveyors of plague, typhoid fever, ...The type III secretion (T3S) injectisome is a specialized protein nanomachine that is critical for the pathogenicity of many Gram-negative bacteria, including purveyors of plague, typhoid fever, whooping cough, sexually transmitted infections and major nosocomial infections. This syringe-shaped 3.5-MDa macromolecular assembly spans both bacterial membranes and that of the infected host cell. The internal channel formed by the injectisome allows for the direct delivery of partially unfolded virulence effectors into the host cytoplasm. The structural foundation of the injectisome is the basal body, a molecular lock-nut structure composed predominantly of three proteins that form highly oligomerized concentric rings spanning the inner and outer membranes. Here we present the structure of the prototypical Salmonella enterica serovar Typhimurium pathogenicity island 1 basal body, determined using single-particle cryo-electron microscopy, with the inner-membrane-ring and outer-membrane-ring oligomers defined at 4.3 Å and 3.6 Å resolution, respectively. This work presents the first, to our knowledge, high-resolution structural characterization of the major components of the basal body in the assembled state, including that of the widespread class of outer-membrane portals known as secretins. | |||||||||
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_8401.map.gz | 35.3 MB | EMDB map data format | |
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Header (meta data) | emd-8401-v30.xml emd-8401.xml | 15.4 KB 15.4 KB | Display Display | EMDB header |
Images | emd_8401.png | 118.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8401 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8401 | HTTPS FTP |
-Validation report
Summary document | emd_8401_validation.pdf.gz | 79.6 KB | Display | EMDB validaton report |
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Full document | emd_8401_full_validation.pdf.gz | 78.7 KB | Display | |
Data in XML | emd_8401_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8401 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8401 | HTTPS FTP |
-Related structure data
Related structure data | 8398C 8399C 8400C 5tcpC 5tcqC 5tcrC C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_8401.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Single particle cryo-EM reconstruction of the Salmonella SPI-1 type III secretion injectisome secretin InvG at 4.4 Angstrom resolution | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.71 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 injectisome basal body
Entire | Name: Type III injectisome basal body |
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Components |
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-Supramolecule #1: Type III injectisome basal body
Supramolecule | Name: Type III injectisome basal body / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: PrgH130-392 mutant |
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Source (natural) | Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) |
Molecular weight | Theoretical: 2 MDa |
-Macromolecule #1: InvG
Macromolecule | Name: InvG / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) |
Sequence | String: MKTHILLARV LACAALVLVT PGYSSEKIPV TGSGFVAKDD SLRTFFDAMA LQLKEPVIVS KMAARKKIT GNFEFHDPNA LLEKLSLQLG LIWYFDGQAI YIYDASEMRN AVVSLRNVSL N EFNNFLKR SGLYNKNYPL RGDNRKGTFY VSGPPVYVDM VVNAATMMDK ...String: MKTHILLARV LACAALVLVT PGYSSEKIPV TGSGFVAKDD SLRTFFDAMA LQLKEPVIVS KMAARKKIT GNFEFHDPNA LLEKLSLQLG LIWYFDGQAI YIYDASEMRN AVVSLRNVSL N EFNNFLKR SGLYNKNYPL RGDNRKGTFY VSGPPVYVDM VVNAATMMDK QNDGIELGRQ KI GVMRLNN TFVGDRTYNL RDQKMVIPGI ATAIERLLQG EEQPLGNIVS SEPPAMPAFS ANG EKGKAA NYAGGMSLQE ALKQNAAAGN IKIVAYPDTN SLLVKGTAEQ VHFIEMLVKA LDVA KRHVE LSLWIVDLNK SDLERLGTSW SGSITIGDKL GVSLNQSSIS TLDGSRFIAA VNALE EKKQ ATVVSRPVLL TQENVPAIFD NNRTFYTKLI GERNVALEHV TYGTMIRVLP RFSADG QIE MSLDIEDGND KTPQSDTTTS VDALPEVGRT LISTIARVPH GKSLLVGGYT RDANTDT VQ SIPFLGKLPL IGSLFRYSSK NKSNVVRVFM IEPKEIVDPL TPDASESVNN ILKQSGAW S GDDKLQKWVR VYLDRGQEAI K |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 10 mg/mL | ||||||||||||
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Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.038 kPa | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 80.0 K / Max: 80.0 K |
Specialist optics | Energy filter - Name: Gatan GIF / Energy filter - Lower energy threshold: 0 eV / Energy filter - Upper energy threshold: 20 eV |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 7676 pixel / Digitization - Dimensions - Height: 7420 pixel / Digitization - Sampling interval: 5.0 µm / Digitization - Frames/image: 1-48 / Number grids imaged: 1 / Number real images: 2685 / Average exposure time: 0.375 sec. / Average electron dose: 1.3 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated defocus max: 3.2 µm / Calibrated defocus min: 1.3 µm / Calibrated magnification: 29240 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 64000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Details | Initial fitting was carried out with Chimera, followed by rebuilding and refinement in Rosetta, Phenix, and Coot. |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT |