[English] 日本語
Yorodumi- EMDB-3564: Subtomogram average of type VI secretion system (T6SS) contracted... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3564 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Subtomogram average of type VI secretion system (T6SS) contracted sheath | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Function / homology | Type VI secretion system TssC-like / TssC1, N-terminal / TssC1, C-terminal / EvpB/VC_A0108, tail sheath N-terminal domain / EvpB/VC_A0108, tail sheath gpW/gp25-like domain / Type VI secretion system sheath protein TssB1 / Type VI secretion system, VipA, VC_A0107 or Hcp2 / Type VI secretion protein / Type VI secretion system contractile sheath small subunit Function and homology information | |||||||||
Biological species | Vibrio cholerae (bacteria) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 17.4 Å | |||||||||
Authors | Wang J / Basler M | |||||||||
Citation | Journal: Nat Microbiol / Year: 2017 Title: Cryo-EM structure of the extended type VI secretion system sheath-tube complex. Authors: Jing Wang / Maximilian Brackmann / Daniel Castaño-Díez / Mikhail Kudryashev / Kenneth N Goldie / Timm Maier / Henning Stahlberg / Marek Basler / Abstract: The bacterial type VI secretion system (T6SS) uses contraction of a long sheath to quickly thrust a tube with associated effectors across membranes of eukaryotic and bacterial cells . Only limited ...The bacterial type VI secretion system (T6SS) uses contraction of a long sheath to quickly thrust a tube with associated effectors across membranes of eukaryotic and bacterial cells . Only limited structural information is available about the inherently unstable precontraction state of the T6SS. Here, we obtain a 3.7 Å resolution structure of a non-contractile sheath-tube complex using cryo-electron microscopy and show that it resembles the extended T6SS inside Vibrio cholerae cells. We build a pseudo-atomic model of the complete sheath-tube assembly, which provides a mechanistic understanding of coupling sheath contraction with pushing and rotating the inner tube for efficient target membrane penetration. Our data further show that sheath contraction exposes a buried recognition domain to specifically trigger the disassembly and recycling of the T6SS sheath by the cognate ATP-dependent unfoldase ClpV. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_3564.map.gz | 3.5 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-3564-v30.xml emd-3564.xml | 9.3 KB 9.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_3564_fsc.xml | 4.3 KB | Display | FSC data file |
Images | emd_3564.png | 114.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3564 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3564 | HTTPS FTP |
-Validation report
Summary document | emd_3564_validation.pdf.gz | 268.2 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_3564_full_validation.pdf.gz | 267.3 KB | Display | |
Data in XML | emd_3564_validation.xml.gz | 7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3564 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3564 | HTTPS FTP |
-Related structure data
Related structure data | 3563C 3566C 3567C 5mxnC 5myuC 5ojqC C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_3564.map.gz / Format: CCP4 / Size: 4.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 5.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Type VI secretion system contracted sheath
Entire | Name: Type VI secretion system contracted sheath |
---|---|
Components |
|
-Supramolecule #1: Type VI secretion system contracted sheath
Supramolecule | Name: Type VI secretion system contracted sheath / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all |
---|---|
Source (natural) | Organism: Vibrio cholerae (bacteria) |
-Macromolecule #1: vipA
Macromolecule | Name: vipA / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
---|---|
Sequence | String: MSKEGSVAPK ERINIKYIPA TGDAQAEVEL PLKTLVVGDF KGHAEQTPLE ERATITVDKN NFEAVMRESE LKITATVKN KLTDDENAEL PVELNFKSLA DFAPDAVASQ VPELKKLIEL REALVALKGP LGNIPAFRER L QSLLNSEE SREKLLAELN LLSGQEEPQA |
-Macromolecule #2: vipB
Macromolecule | Name: vipB / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
---|---|
Sequence | String: MMSTTEKVLE RPQLAQGSLL DEIMAQTRIA PSEEGYDIAK KGVAAFIENL MGSQHSAEPV NKSLVDQMLV ELDKKISAQ MDEILHNSQF QAMESAWRGL KLFVDRTDFR ENNKVEILHV TKDELLEDFE FAPETAQSGL Y KHVYSAGY GQFGGEPVGA IIGNYAFTPS ...String: MMSTTEKVLE RPQLAQGSLL DEIMAQTRIA PSEEGYDIAK KGVAAFIENL MGSQHSAEPV NKSLVDQMLV ELDKKISAQ MDEILHNSQF QAMESAWRGL KLFVDRTDFR ENNKVEILHV TKDELLEDFE FAPETAQSGL Y KHVYSAGY GQFGGEPVGA IIGNYAFTPS TPDMKLLQYM GALGAMAHAP FISSVGPEFF GIDSFEELPN IK DLKSTFE SPKYTKWRSL RESEDARYLG LTAPRFLLRV PYDPIENPVK SFNYAENVSA SHEHYLWGNT AFA FATRLT DSFAKYRWCP NIIGPQSGGA VEDLPVHVFE SMGALQSKIP TEVLITDRKE FELAEEGFIA LTMR KGSDN AAFFSANSIQ KPKVFPNTKE GKEAETNYKL GTQLPYMMII NRLAHYVKVL QREQIGAWKE RQDLE RELN SWIKQYVADQ ENPPADVRSR RPLRAARIEV MDVEGNPGWY QVSLSVRPHF KYMGANFELS LVGRLD QA |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | subtomogram averaging |
Aggregation state | helical array |
-Sample preparation
Buffer | pH: 7.5 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.0 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 |