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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: 3600
TitleContracted sheath of a Pseudomonas aeruginosa type six secretion system consisting of TssB1 and TssC1
Map data
Samplecontracted sheath of a Pseudomonas aeruginosa T6SS consisting of TssB1 and TssC1
  • AO964_32215, PAERUG_E15_London_28_01_14_04448, PAERUG_P32_London_17_VIM_2_10_11_02574, PAMH19_0082
  • U769_00445
  • Type VI secretion protein, familyType VI secretion system
  • EvpB family type VI secretion proteinType VI secretion system
Function / homologyType VI secretion system, VipA, VC_A0107 or Hcp2 / Type VI secretion protein, EvpB/VC_A0108, tail sheath / Type VI secretion system, VipA, VC_A0107 or Hcp2 / Type VI secretion protein, EvpB/VC_A0108, tail sheath / Type VI secretion protein / EvpB family type VI secretion protein / Uncharacterized protein / Uncharacterized protein
Function and homology information
SourcePseudomonas aeruginosa (bacteria)
Methodhelical reconstruction / cryo EM / 3.28 Å resolution
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.
Validation ReportPDB-ID: 5n8n

SummaryFull reportAbout validation report
DateDeposition: Feb 23, 2017 / Header (metadata) release: Mar 29, 2017 / Map release: Jan 10, 2018 / Last update: Feb 14, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0385
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0385
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5n8n
  • Surface level: 0.0385
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-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

Fileemd_3600.map.gz (map file in CCP4 format, 62501 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
250 pix
1.34 Å/pix.
= 335. Å		250 pix
1.34 Å/pix.
= 335. Å		250 pix
1.34 Å/pix.
= 335. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34 Å
Density

Histogram

Histogram (log scale)
Contour Level:0.0385 (by author), 0.0385 (movie #1):
Minimum - Maximum-0.28614312 - 0.5116937
Average (Standard dev.)0.0024665967 (0.029884944)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions250250250
Origin0.00.00.0
Limit249.0249.0249.0
Spacing250250250
CellA=B=C: 335.0 Å
α=β=γ: 90.0 deg.

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
start NX/NY/NZ
NX/NY/NZ
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
Number of components: 5

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Component #1: protein, contracted sheath of a Pseudomonas aeruginosa T6SS consi...

ProteinName: contracted sheath of a Pseudomonas aeruginosa T6SS consisting of TssB1 and TssC1
Recombinant expression: No

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Component #2: protein, AO964_32215, PAERUG_E15_London_28_01_14_04448, PAERUG_P3...

ProteinName: AO964_32215, PAERUG_E15_London_28_01_14_04448, PAERUG_P32_London_17_VIM_2_10_11_02574, PAMH19_0082
Recombinant expression: No
SourceSpecies: Pseudomonas aeruginosa (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #3: protein, U769_00445

ProteinName: U769_00445 / Recombinant expression: No
SourceSpecies: Pseudomonas aeruginosa (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #4: protein, Type VI secretion protein, family

ProteinName: Type VI secretion protein, familyType VI secretion system
Number of Copies: 15 / Recombinant expression: No
MassTheoretical: 14.634741 kDa
SourceSpecies: Pseudomonas aeruginosa (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #5: protein, EvpB family type VI secretion protein

ProteinName: EvpB family type VI secretion proteinType VI secretion system
Number of Copies: 15 / Recombinant expression: No
MassTheoretical: 51.721125 kDa
SourceSpecies: Pseudomonas aeruginosa (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenSpecimen state: helical array / Method: cryo EM
Helical parametersAxial symmetry: C1 (asymmetric) / Delta z: 20.2 Å / Delta phi: 27.7 deg.
Sample solutionSpecimen conc.: 1 mg/ml / pH: 9
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 3 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: helical reconstruction
3D reconstructionResolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

5n8n

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