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Yorodumi- EMDB-22589: Cryo-EM structure of the nonameric EscV cytosolic domain from the... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22589 | ||||||||||||
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Title | Cryo-EM structure of the nonameric EscV cytosolic domain from the type III secretion system | ||||||||||||
Map data | |||||||||||||
Sample |
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Keywords | Injectisome / Nonamer / Export Apparatus / Secretion / PROTEIN TRANSPORT | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | Escherichia coli O127:H6 str. E2348/69 (bacteria) / Escherichia coli O127:H6 (strain E2348/69 / EPEC) (bacteria) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.7 Å | ||||||||||||
Authors | Majewski DD / Lyons BJE | ||||||||||||
Funding support | Canada, 3 items
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Citation | Journal: J Struct Biol / Year: 2020 Title: Cryo-EM analysis of the SctV cytosolic domain from the enteropathogenic E. coli T3SS injectisome. Authors: Dorothy D Majewski / Bronwyn J E Lyons / Claire E Atkinson / Natalie C J Strynadka / Abstract: The bacterial injectisome and flagella both rely on type III secretion systems for their assembly. The syringe-like injectisome creates a continuous channel between the bacterium and the host cell, ...The bacterial injectisome and flagella both rely on type III secretion systems for their assembly. The syringe-like injectisome creates a continuous channel between the bacterium and the host cell, through which signal-modulating effector proteins are secreted. The inner membrane pore protein SctV controls the hierarchy of substrate selection and may also be involved in energizing secretion. We present the 4.7 Å cryo-EM structure of the SctV cytosolic domain (SctV) from the enteropathogenic Escherichia coli injectisome. SctV forms a nonameric ring with primarily electrostatic interactions between its subunits. Molecular dynamics simulations show that monomeric SctV maintains a closed conformation, in contrast with previous studies on flagellar homologue FlhA. Comparison with substrate-bound homologues suggest that a conformational change would be required to accommodate binding partners. | ||||||||||||
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_22589.map.gz | 14.5 MB | EMDB map data format | |
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Header (meta data) | emd-22589-v30.xml emd-22589.xml | 11.1 KB 11.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_22589_fsc.xml | 11.4 KB | Display | FSC data file |
Images | emd_22589.png | 67.8 KB | ||
Filedesc metadata | emd-22589.cif.gz | 5.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22589 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22589 | HTTPS FTP |
-Validation report
Summary document | emd_22589_validation.pdf.gz | 429.2 KB | Display | EMDB validaton report |
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Full document | emd_22589_full_validation.pdf.gz | 428.7 KB | Display | |
Data in XML | emd_22589_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | emd_22589_validation.cif.gz | 16.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22589 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22589 | HTTPS FTP |
-Related structure data
Related structure data | 7k08MC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_22589.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 0.852 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 : EscV Cytosolic Nonamer Ring
Entire | Name: EscV Cytosolic Nonamer Ring |
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Components |
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-Supramolecule #1: EscV Cytosolic Nonamer Ring
Supramolecule | Name: EscV Cytosolic Nonamer Ring / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Escherichia coli O127:H6 str. E2348/69 (bacteria) |
Molecular weight | Theoretical: 350 KDa |
-Macromolecule #1: Translocator EscV
Macromolecule | Name: Translocator EscV / type: protein_or_peptide / ID: 1 / Number of copies: 9 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli O127:H6 (strain E2348/69 / EPEC) (bacteria) Strain: E2348/69 / EPEC |
Molecular weight | Theoretical: 39.081633 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: GSHMADLSNS QNISPGAEPL ILNLSSNIYS SDITQQIEVM RWNFFEESGI PLPKIIVNPV KNNDSAIEFL LYQESIYKDT LIDDTVYFE AGHAEISFEF VQEKLSTNSI VYKTNKTNQQ LAHLTGMDVY ATTNDKITFL LKKLVLSNAK EFIGVQETRY L MDIMERKY ...String: GSHMADLSNS QNISPGAEPL ILNLSSNIYS SDITQQIEVM RWNFFEESGI PLPKIIVNPV KNNDSAIEFL LYQESIYKDT LIDDTVYFE AGHAEISFEF VQEKLSTNSI VYKTNKTNQQ LAHLTGMDVY ATTNDKITFL LKKLVLSNAK EFIGVQETRY L MDIMERKY NELVKELQRQ LGLSKIVDIL QRLVEENVSI RDLRTIFETL IFWSTKEKDV VILCEYVRIA LRRHILGRYS VS GTLLNVW LIGSDIENEL RESIRQTSSG SYLNISPERT EQIIGFLKNI MNPTGNGVIL TALDIRRYVK KMIEGSFPSV PVL SFQEVG NNIELKVLGT VNDFRA UniProtKB: Translocator EscV |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.5 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 60.0 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 |