+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4898 | |||||||||
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Title | TssA protein from T6SS of Vibrio cholerae. | |||||||||
Map data | ||||||||||
Sample |
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Keywords | T6SS / Vibrio / TssA / cap / TRANSPORT PROTEIN | |||||||||
Function / homology | Type VI secretion system-associated, VCA0119 / Type VI secretion, EvfE, EvfF, ImpA, BimE, VC_A0119, VasJ / ImpA, N-terminal / ImpA, N-terminal, type VI secretion system / Type VI secretion system protein TssA / ImpA_N domain-containing protein Function and homology information | |||||||||
Biological species | Vibrio cholerae (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Nazarov S / Adaixo R / Basler M | |||||||||
Funding support | Switzerland, 1 items
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Citation | Journal: EMBO J / Year: 2019 Title: Diverse roles of TssA-like proteins in the assembly of bacterial type VI secretion systems. Authors: Johannes Paul Schneider / Sergey Nazarov / Ricardo Adaixo / Martina Liuzzo / Peter David Ringel / Henning Stahlberg / Marek Basler / Abstract: Protein translocation by the bacterial type VI secretion system (T6SS) is driven by a rapid contraction of a sheath assembled around a tube with associated effectors. Here, we show that TssA-like or ...Protein translocation by the bacterial type VI secretion system (T6SS) is driven by a rapid contraction of a sheath assembled around a tube with associated effectors. Here, we show that TssA-like or TagA-like proteins with a conserved N-terminal domain and varying C-terminal domains can be grouped into at least three distinct classes based on their role in sheath assembly. The proteins of the first class increase speed and frequency of sheath assembly and form a stable dodecamer at the distal end of a polymerizing sheath. The proteins of the second class localize to the cell membrane and block sheath polymerization upon extension across the cell. This prevents excessive sheath polymerization and bending, which may result in sheath destabilization and detachment from its membrane anchor and thus result in failed secretion. The third class of these proteins localizes to the baseplate and is required for initiation of sheath assembly. Our work shows that while various proteins share a conserved N-terminal domain, their roles in T6SS biogenesis are fundamentally different. | |||||||||
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_4898.map.gz | 100 MB | EMDB map data format | |
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Header (meta data) | emd-4898-v30.xml emd-4898.xml | 22.6 KB 22.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4898_fsc.xml | 11.5 KB | Display | FSC data file |
Images | emd_4898.png | 179.6 KB | ||
Masks | emd_4898_msk_1.map | 129.7 MB | Mask map | |
Filedesc metadata | emd-4898.cif.gz | 6.3 KB | ||
Others | emd_4898_additional_1.map.gz emd_4898_additional_2.map.gz emd_4898_additional_3.map.gz emd_4898_half_map_1.map.gz emd_4898_half_map_2.map.gz | 7.5 MB 119.8 MB 120.9 MB 100.4 MB 100.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4898 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4898 | HTTPS FTP |
-Validation report
Summary document | emd_4898_validation.pdf.gz | 676.7 KB | Display | EMDB validaton report |
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Full document | emd_4898_full_validation.pdf.gz | 676.3 KB | Display | |
Data in XML | emd_4898_validation.xml.gz | 18.6 KB | Display | |
Data in CIF | emd_4898_validation.cif.gz | 24.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4898 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4898 | HTTPS FTP |
-Related structure data
Related structure data | 6riuMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10271 (Title: Cryo electron microscopy of TssA protein from T6SS of Vibrio cholerae. Data size: 1.3 TB Data #1: Frame-averaged micrographs of TssA protein from T6SS of Vibrio cholerae [micrographs - single frame] Data #2: Aligned multi-frame micrographs of TssA protein from T6SS of Vibrio cholerae [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_4898.map.gz / Format: CCP4 / Size: 129.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.058 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_4898_msk_1.map | ||||||||||||
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-Additional map: #1
File | emd_4898_additional_1.map | ||||||||||||
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-Additional map: #3
File | emd_4898_additional_2.map | ||||||||||||
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-Additional map: #2
File | emd_4898_additional_3.map | ||||||||||||
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-Half map: #2
File | emd_4898_half_map_1.map | ||||||||||||
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-Half map: #1
File | emd_4898_half_map_2.map | ||||||||||||
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Density Histograms |
-Sample components
-Entire : Type VI secretion system protein TssA.
Entire | Name: Type VI secretion system protein TssA. |
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Components |
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-Supramolecule #1: Type VI secretion system protein TssA.
Supramolecule | Name: Type VI secretion system protein TssA. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Vibrio cholerae (bacteria) |
Molecular weight | Theoretical: 634 KDa |
-Supramolecule #2: Middle N-terminal domain (Nt2) of TssA protein from T6SS of Vibri...
Supramolecule | Name: Middle N-terminal domain (Nt2) of TssA protein from T6SS of Vibrio cholerae. type: complex / ID: 2 / Parent: 1 / Macromolecule list: all |
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Source (natural) | Organism: Vibrio cholerae (bacteria) |
-Macromolecule #1: Type VI secretion system protein TssA
Macromolecule | Name: Type VI secretion system protein TssA / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Vibrio cholerae (bacteria) |
Molecular weight | Theoretical: 53.102793 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MEMTEYRQCV AKPISSSNPV GERLVDHPLF DFIEDQMMKV GSLSHASVQW DEVEHSTLKL LGEQSKDIKL LVYLLQCLHN QVTPTRLIT SFAVMSEFLN QYWNDSYPAP GARGNLPRRK FFSQMAQRFT TVIEKFDFHH LDEADRQALQ AAVEEWQQAV E KQGLSSEL ...String: MEMTEYRQCV AKPISSSNPV GERLVDHPLF DFIEDQMMKV GSLSHASVQW DEVEHSTLKL LGEQSKDIKL LVYLLQCLHN QVTPTRLIT SFAVMSEFLN QYWNDSYPAP GARGNLPRRK FFSQMAQRFT TVIEKFDFHH LDEADRQALQ AAVEEWQQAV E KQGLSSEL VESVVVRITA EIKRAEQRQQ VTAQSSAERE TPSAATSSPA ASMVVDHSSD KAAKQTLLKV ADFLAEQEFG IA LSIRLRR FAVWGSITSL PDHKPDGETL LRGMQADRVK DYQDQLRHPD LALWRKVEQS LTMAPYWFEG QWMSYTIAQQ LGK SDWCQA IAEETQQFLR RLPSLLELKF KGGEPFVSDS VKEWLASVGQ SQGAAGQSVG GDWQEKRKEA FQLAKEGGIA VALS MLNDG LVSAVEPRDK FYWRLLSADL LRANHLDAMA GEQYQTLLNQ VTTLSVPEWE PSLVEQIQRY TTSE UniProtKB: Type VI secretion system protein TssA |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: LACEY |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 293 K / Details: Leica EM GP2. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum LS |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 2963 / 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 / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |