+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0010 | |||||||||
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Title | The baseplate complex from the type VI secretion system | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Secretion / baseplate / complex / STRUCTURAL PROTEIN | |||||||||
Function / homology | Type VI secretion, TssG-like / Type VI secretion, TssG / Type VI secretion system TssK / Bacterial Type VI secretion, VC_A0110, EvfL, ImpJ, VasE / Type VI secretion system baseplate subunit TssG / Type VI secretion system protein ImpH / Uncharacterized protein Function and homology information | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.3 Å | |||||||||
Authors | Rapisarda C / Fronzes R | |||||||||
Citation | Journal: Nat Microbiol / Year: 2018 Title: Biogenesis and structure of a type VI secretion baseplate. Authors: Yassine Cherrak / Chiara Rapisarda / Riccardo Pellarin / Guillaume Bouvier / Benjamin Bardiaux / Fabrice Allain / Christian Malosse / Martial Rey / Julia Chamot-Rooke / Eric Cascales / Rémi ...Authors: Yassine Cherrak / Chiara Rapisarda / Riccardo Pellarin / Guillaume Bouvier / Benjamin Bardiaux / Fabrice Allain / Christian Malosse / Martial Rey / Julia Chamot-Rooke / Eric Cascales / Rémi Fronzes / Eric Durand / Abstract: To support their growth in a competitive environment and cause pathogenesis, bacteria have evolved a broad repertoire of macromolecular machineries to deliver specific effectors and toxins. Among ...To support their growth in a competitive environment and cause pathogenesis, bacteria have evolved a broad repertoire of macromolecular machineries to deliver specific effectors and toxins. Among these multiprotein complexes, the type VI secretion system (T6SS) is a contractile nanomachine that targets both prokaryotic and eukaryotic cells. The T6SS comprises two functional subcomplexes: a bacteriophage-related tail structure anchored to the cell envelope by a membrane complex. As in other contractile injection systems, the tail is composed of an inner tube wrapped by a sheath and built on the baseplate. In the T6SS, the baseplate is not only the tail assembly platform, but also docks the tail to the membrane complex and hence serves as an evolutionary adaptor. Here we define the biogenesis pathway and report the cryo-electron microscopy (cryo-EM) structure of the wedge protein complex of the T6SS from enteroaggregative Escherichia coli (EAEC). Using an integrative approach, we unveil the molecular architecture of the whole T6SS baseplate and its interaction with the tail sheath, offering detailed insights into its biogenesis and function. We discuss architectural and mechanistic similarities but also reveal key differences with the T4 phage and Mu phage baseplates. | |||||||||
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_0010.map.gz | 323 MB | EMDB map data format | |
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Header (meta data) | emd-0010-v30.xml emd-0010.xml | 11.8 KB 11.8 KB | Display Display | EMDB header |
Images | emd_0010.png | 60.8 KB | ||
Filedesc metadata | emd-0010.cif.gz | 5.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0010 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0010 | HTTPS FTP |
-Validation report
Summary document | emd_0010_validation.pdf.gz | 284.6 KB | Display | EMDB validaton report |
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Full document | emd_0010_full_validation.pdf.gz | 283.7 KB | Display | |
Data in XML | emd_0010_validation.xml.gz | 7.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0010 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0010 | HTTPS FTP |
-Related structure data
Related structure data | 6gj3MC 0008C 0009C 6giyC 6gj1C 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_0010.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.1 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 : Complex of TssK, TssF and TssG, components of the type VI secreti...
Entire | Name: Complex of TssK, TssF and TssG, components of the type VI secretion system baseplate |
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Components |
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-Supramolecule #1: Complex of TssK, TssF and TssG, components of the type VI secreti...
Supramolecule | Name: Complex of TssK, TssF and TssG, components of the type VI secretion system baseplate type: cell / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: TssG
Macromolecule | Name: TssG / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 29.983488 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MPAHYISDIA QQREGHEAAA DFLDIFSHRL ITQYYRIWRK YSYPATFEAG GQDKTSQYLL GLARLGIPGC AQNIATPVSR FLALLPLML LPGRTAEGLT SLVTLLAPGT QARVWHHDRR RIPLKTPLTM RVHHPVSLKS RPVMGDHATD VNGQVLLQLS T QTGSEVQG ...String: MPAHYISDIA QQREGHEAAA DFLDIFSHRL ITQYYRIWRK YSYPATFEAG GQDKTSQYLL GLARLGIPGC AQNIATPVSR FLALLPLML LPGRTAEGLT SLVTLLAPGT QARVWHHDRR RIPLKTPLTM RVHHPVSLKS RPVMGDHATD VNGQVLLQLS T QTGSEVQG WLPGGHLYSD LLALLHVYLG SRLDVRLQLC VERSLLPDAR LSCRPAAGSP QLGRTAVMRT QAKITTSAAR VM TISLGRY QRVQEHYQRK ETQENGDYRW UniProtKB: Type VI secretion system protein ImpH |
-Macromolecule #2: TssK
Macromolecule | Name: TssK / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 49.999223 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MKIYRPLWED GAFLMPQQFQ QQAAWDVHLA DSVARMGLAH PWGVVAAEFD DSLLPLSRLN ATRLIVRFPD GTLIDTERAD NLPPVCDLS TVSDRSLVDI VLALPLLNAN GGNLDNGSES ERPRRWKSER VNVQELAGHE QSEVAVLRHN LTLRMAHQEN A AWLTCPVT ...String: MKIYRPLWED GAFLMPQQFQ QQAAWDVHLA DSVARMGLAH PWGVVAAEFD DSLLPLSRLN ATRLIVRFPD GTLIDTERAD NLPPVCDLS TVSDRSLVDI VLALPLLNAN GGNLDNGSES ERPRRWKSER VNVQELAGHE QSEVAVLRHN LTLRMAHQEN A AWLTCPVT RLVRDAQGQW CRDPRFIPPL LTLSASPSLM TELLELLHHL QARRQRLMSM RRENNARLAD FAVADVSLFW LL NALNSAE PVLKELLDMP YRHPELLYRE LARLAGSLLT FSLEHNVDAV PAYHHETPEN VFPPLLSLLN RLLEASLPSR VVF IELKQK GVMWEGALHD ARLREGADFW LSVRSSMPGH ELQTKFPQLC KAGSPDDVSE VVNVALSGVI IRPVTHVPAA IPLR LENQY FALDLSTDAA RAMLDAGRCT FYTPASLGDV KLELFAVLRT UniProtKB: Uncharacterized protein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.2 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated defocus max: 3.0 µm / Calibrated defocus min: 0.4 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 130000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 32504 |
Initial angle assignment | Type: RANDOM ASSIGNMENT / Software - Name: cryoSPARC |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | PDB-6gj3: |