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- EMDB-3600: Contracted sheath of a Pseudomonas aeruginosa type six secretion ... -

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Basic information

Entry
Database: EMDB / ID: EMD-3600
TitleContracted sheath of a Pseudomonas aeruginosa type six secretion system consisting of TssB1 and TssC1
Map data
Sample
  • Complex: contracted sheath of a Pseudomonas aeruginosa T6SS consisting of TssB1 and TssC1
    • Complex: AO964_32215, PAERUG_E15_London_28_01_14_04448, PAERUG_P32_London_17_VIM_2_10_11_02574, PAMH19_0082
      • Protein or peptide: Type VI secretion protein, familyType VI secretion system
    • Complex: U769_00445
      • Protein or peptide: EvpB family type VI secretion proteinType VI secretion system
Function / homology
Function and homology information


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
Similarity search - Domain/homology
Type VI secretion protein / : / Type VI secretion system sheath protein TssC1 / Type VI secretion system sheath protein TssB1
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsSalih O / He S / Stach L / Macdonald JT / Planamente S / Manoli E / Scheres S / Filloux A / Freemont PS
CitationJournal: Structure / Year: 2018
Title: Atomic Structure of Type VI Contractile Sheath from Pseudomonas aeruginosa.
Authors: Osman Salih / Shaoda He / Sara Planamente / Lasse Stach / James T MacDonald / Eleni Manoli / Sjors H W Scheres / Alain Filloux / Paul S Freemont /
Abstract: Pseudomonas aeruginosa has three type VI secretion systems (T6SSs), H1-, H2-, and H3-T6SS, each belonging to a distinct group. The two T6SS components, TssB/VipA and TssC/VipB, assemble to form ...Pseudomonas aeruginosa has three type VI secretion systems (T6SSs), H1-, H2-, and H3-T6SS, each belonging to a distinct group. The two T6SS components, TssB/VipA and TssC/VipB, assemble to form tubules that conserve structural/functional homology with tail sheaths of contractile bacteriophages and pyocins. Here, we used cryoelectron microscopy to solve the structure of the H1-T6SS P. aeruginosa TssB1C1 sheath at 3.3 Å resolution. Our structure allowed us to resolve some features of the T6SS sheath that were not resolved in the Vibrio cholerae VipAB and Francisella tularensis IglAB structures. Comparison with sheath structures from other contractile machines, including T4 phage and R-type pyocins, provides a better understanding of how these systems have conserved similar functions/mechanisms despite evolution. We used the P. aeruginosa R2 pyocin as a structural template to build an atomic model of the TssB1C1 sheath in its extended conformation, allowing us to propose a coiled-spring-like mechanism for T6SS sheath contraction.
History
DepositionFeb 23, 2017-
Header (metadata) releaseMar 29, 2017-
Map releaseJan 10, 2018-
UpdateFeb 14, 2018-
Current statusFeb 14, 2018Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0385
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0385
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5n8n
  • Surface level: 0.0385
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5n8n
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3600.png

Downloads & links

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Map

FileDownload / File: emd_3600.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.34 Å
Density
Contour LevelBy AUTHOR: 0.0385 / Movie #1: 0.0385
Minimum - Maximum-0.28614312 - 0.5116937
Average (Standard dev.)0.0024665967 (±0.029884944)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 335.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.341.341.34
M x/y/z250250250
origin x/y/z0.0000.0000.000
length x/y/z335.000335.000335.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS250250250
D min/max/mean-0.2860.5120.002

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Supplemental data

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Sample components

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Entire : contracted sheath of a Pseudomonas aeruginosa T6SS consisting of ...

EntireName: contracted sheath of a Pseudomonas aeruginosa T6SS consisting of TssB1 and TssC1
Components
  • Complex: contracted sheath of a Pseudomonas aeruginosa T6SS consisting of TssB1 and TssC1
    • Complex: AO964_32215, PAERUG_E15_London_28_01_14_04448, PAERUG_P32_London_17_VIM_2_10_11_02574, PAMH19_0082
      • Protein or peptide: Type VI secretion protein, familyType VI secretion system
    • Complex: U769_00445
      • Protein or peptide: EvpB family type VI secretion proteinType VI secretion system

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Supramolecule #1: contracted sheath of a Pseudomonas aeruginosa T6SS consisting of ...

SupramoleculeName: contracted sheath of a Pseudomonas aeruginosa T6SS consisting of TssB1 and TssC1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: AO964_32215, PAERUG_E15_London_28_01_14_04448, PAERUG_P32_London_...

SupramoleculeName: AO964_32215, PAERUG_E15_London_28_01_14_04448, PAERUG_P32_London_17_VIM_2_10_11_02574, PAMH19_0082
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Supramolecule #3: U769_00445

SupramoleculeName: U769_00445 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: Type VI secretion protein, family

MacromoleculeName: Type VI secretion protein, family / type: protein_or_peptide / ID: 1 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 14.634741 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
TTSSQKFIAR NRAPRVQIEY DVELYGAEKK VQLPFVMGVM ADLAGKPAEP QAAVADRKFL EIDVDNFDAR LKAMKPRVAF NVPNVLTGE GNLSLDITFE SMDDFSPAAV ARKVDSLNKL LEARTQLANL LTY

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Macromolecule #2: EvpB family type VI secretion protein

MacromoleculeName: EvpB family type VI secretion protein / type: protein_or_peptide / ID: 2 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 51.721125 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: REAVETAVRT LAEHALEQTS LISNDAIKSI ESIIAALDAK LTAQVNLIMH HADFQQLESA WRGLHYLVNN TETDEQLKIR VLNISKPEL HKTLKKFKGT TWDQSPIFKK LYEEEYGQFG GEPYGCLVGD YYFDQSPPDV ELLGEMAKIS AAMHAPFISA A SPTVMGMG ...String:
REAVETAVRT LAEHALEQTS LISNDAIKSI ESIIAALDAK LTAQVNLIMH HADFQQLESA WRGLHYLVNN TETDEQLKIR VLNISKPEL HKTLKKFKGT TWDQSPIFKK LYEEEYGQFG GEPYGCLVGD YYFDQSPPDV ELLGEMAKIS AAMHAPFISA A SPTVMGMG SWQELSNPRD LTKIFTTPEY AGWRSLRESE DSRYIGLTMP RFLARLPYGA KTDPVEEFAF EEETDGADSS KY AWANSAY AMAVNINRSF KLYGWCSRIR GVESGGEVQG LPAHTFPTDD GGVDMKCPTE IAISDRREAE LAKNGFMPLL HKK NTDFAA FIGAQSLQKP AEYDDPDATA NANLAARLPY LFATCRFAHY LKCIVRDKIG SFKEKDEMQR WLQDWILNYV DGDP AHSTE TTKAQHPLAA AEVVVEEVEG NPGYYNSKFF LRPHYQLEGL TVSLRLVSKL PSAKEA

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

Concentration1 mg/mL
BufferpH: 9
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 30.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Helical parameters - Δz: 20.2 Å
Applied symmetry - Helical parameters - Δ&Phi: 27.7 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 71264

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