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- EMDB-0010: The baseplate complex from the type VI secretion system -

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Basic information

Entry
Database: EMDB / ID: EMD-0010
TitleThe baseplate complex from the type VI secretion system
Map data
Sample
  • Cell: Complex of TssK, TssF and TssG, components of the type VI secretion system baseplate
    • Protein or peptide: TssG
    • Protein or peptide: TssK
Function / homologyType 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 speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsRapisarda C / Fronzes R
CitationJournal: 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
DepositionMay 15, 2018-
Header (metadata) releaseJun 20, 2018-
Map releaseOct 17, 2018-
UpdateDec 18, 2019-
Current statusDec 18, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 6
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 6
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6gj3
  • Surface level: 6
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0010.png

Downloads & links

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Map

FileDownload / File: emd_0010.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 6 / Movie #1: 6
Minimum - Maximum-13.500279 - 32.492695
Average (Standard dev.)0.00000000000 (±1)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 495.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z450450450
origin x/y/z0.0000.0000.000
length x/y/z495.000495.000495.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS450450450
D min/max/mean-13.50032.4930.000

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Supplemental data

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Sample components

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Entire : Complex of TssK, TssF and TssG, components of the type VI secreti...

EntireName: Complex of TssK, TssF and TssG, components of the type VI secretion system baseplate
Components
  • Cell: Complex of TssK, TssF and TssG, components of the type VI secretion system baseplate
    • Protein or peptide: TssG
    • Protein or peptide: TssK

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Supramolecule #1: Complex of TssK, TssF and TssG, components of the type VI secreti...

SupramoleculeName: Complex of TssK, TssF and TssG, components of the type VI secretion system baseplate
type: cell / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: TssG

MacromoleculeName: TssG / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 29.983488 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: 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

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Macromolecule #2: TssK

MacromoleculeName: TssK / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 49.999223 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: 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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.2 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 3.0 µm / Calibrated defocus min: 0.4 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.7 µm / Nominal magnification: 130000
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.5 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 32504

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-6gj3:
The baseplate complex from the type VI secretion system

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