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- EMDB-0009: The baseplate complex from the type VI secretion system -

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Basic information

Entry
Database: EMDB / ID: EMD-0009
TitleThe baseplate complex from the type VI secretion system
Map data
Sample
  • Complex: Type VI secretion system baseplate complex
    • Protein or peptide: Putative type VI secretion protein
    • Protein or peptide: TssG
    • Protein or peptide: TssE
KeywordsSecretion / baseplate / complex / STRUCTURAL PROTEIN
Function / homology
Function and homology information


Type VI secretion system protein TssE1-like / Type VI secretion system TssF / Type VI secretion system, TssF / Type VI secretion, TssG-like / Type VI secretion, TssG / IraD/Gp25-like / Baseplate wedge protein gp25
Similarity search - Domain/homology
IraD/Gp25-like domain-containing protein / Type VI secretion system baseplate subunit TssG / Type VI secretion system baseplate subunit TssF / Type VI secretion protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.7 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-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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Structure visualization

Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0009.png

Downloads & links

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Map

FileDownload / File: emd_0009.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.1 Å/pix.
x 200 pix.
= 220. Å		1.1 Å/pix.
x 200 pix.
= 220. Å		1.1 Å/pix.
x 200 pix.
= 220. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.5
Minimum - Maximum-9.079955999999999 - 16.808064999999999
Average (Standard dev.)-0.00000000000268 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 220.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Type VI secretion system baseplate complex

EntireName: Type VI secretion system baseplate complex
Components
  • Complex: Type VI secretion system baseplate complex
    • Protein or peptide: Putative type VI secretion protein
    • Protein or peptide: TssG
    • Protein or peptide: TssE

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Supramolecule #1: Type VI secretion system baseplate complex

SupramoleculeName: Type VI secretion system baseplate complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Putative type VI secretion protein

MacromoleculeName: Putative type VI secretion protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 66.557125 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MDDLTLRYFD AEMRYLREAG KAFAQAHPDR AAMLDLDKAG TPDPCVERLF EGFAFSMGRL RQKIDDDLPE LTESLVSMLW PHYLRTIPS LSVVALTPRL SVMKMAETVP AGLEVTSRPV GPGNTVCRYR TTRAIPLNPL AVEKVVMTTE PDGRSVLKIG F ACSELADW ...String:
MDDLTLRYFD AEMRYLREAG KAFAQAHPDR AAMLDLDKAG TPDPCVERLF EGFAFSMGRL RQKIDDDLPE LTESLVSMLW PHYLRTIPS LSVVALTPRL SVMKMAETVP AGLEVTSRPV GPGNTVCRYR TTRAIPLNPL AVEKVVMTTE PDGRSVLKIG F ACSELADW SQVDLHRLSL YLAAEAPVSS TLHLMMTKRL AALYLRLPGN DERIRIDGWF SPGGFAEEDR LWPKGDSAFS GY QLLLEYF TFREKFMFVH LNGLENVSLP AGISGFDLEV VLSQPWPADL PVTDDALCLH CVPVINLFTL EADPLIINGL ESE YLLRPK RLQDGYTEIY SVDAVTGSGR TGSAEYVPFT SFRHRGGMLR HDAPERYYHT RVKRGVTGMY DTWLILGGQR WEAD RMPER ETLSLRITGT NGQLPRRALQ STLLDRCEQV LQAPVSVRNL CKPTLPVYPP TEDRFHWRVM SHLGTGFLNM LSSAE VLRG TLALYNWRDD ELNHRRLDAI LAVQHHRIQR FEKGFLLRGL DVEVTLDGNG FAGEGDIHLF GEMLNRFLAL YADMNQ FNQ LTLIVQPEGK CIRWKENHNP RLPG

UniProtKB: Type VI secretion protein

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Macromolecule #2: TssG

MacromoleculeName: TssG / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 41.216344 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MHPVERKSQS APARLITRYR KQLPYINFYR FCQLLEQSQP DQPPIGSGWQ ARQEAVRFCP YPGMGFPASE IKDAVIPEES HLPPIVHVT FMGLYGVTSP LPAHYISDIA QQREGHEAAA DFLDIFSHRL ITQYYRIWRK YSYPATFEAG GQDKTSQYLL G LARLGIPG ...String:
MHPVERKSQS APARLITRYR KQLPYINFYR FCQLLEQSQP DQPPIGSGWQ ARQEAVRFCP YPGMGFPASE IKDAVIPEES HLPPIVHVT FMGLYGVTSP LPAHYISDIA QQREGHEAAA DFLDIFSHRL ITQYYRIWRK YSYPATFEAG GQDKTSQYLL G LARLGIPG CAQNIATPVS RFLALLPLML LPGRTAEGLT SLVTLLAPGT QARVWHHDRR RIPLKTPLTM RVHHPVSLKS RP VMGDHAT DVNGQVLLQL STQTGSEVQG WLPGGHLYSD LLALLHVYLG SRLDVRLQLC VERSLLPDAR LSCRPAAGSP QLG RTAVMR TQAKIATSAA RVMTISLGRY QRVQEHYQRK ETQENGDYRW

UniProtKB: Type VI secretion system baseplate subunit TssG

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Macromolecule #3: TssE

MacromoleculeName: TssE / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 16.320783 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MPRPSLYEIL YGNFTGGLEL NQVGEEEQVI LSVLDNMQRI LNTRAGSLKH LPDYGLPDIT TILQGMPGTA HQLMRVLSDV LLKYEPRIK RVDVTMQEQT QPGELHYVID AELKDAGLVR YGTTFIPEGR VLLRHLKQQR YVQT

UniProtKB: IraD/Gp25-like domain-containing protein

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 32504
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION

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