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- EMDB-6271: Atomic structures of a bactericidal contractile nanotube in its p... -

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Basic information

Entry
Database: EMDB / ID: EMD-6271
TitleAtomic structures of a bactericidal contractile nanotube in its pre- and post-contraction states
Map dataPyocin, contracted sheath
Sample
  • Sample: Pyocin (post-contraction)
  • Protein or peptide: pyocin tail sheath
Keywordspyocin / bacteriocin / sheath / tube
Function / homology: / Tail sheath protein Gp18 domain III N-terminal region / : / Tail sheath protein, subtilisin-like domain / Phage tail sheath protein subtilisin-like domain / Tail sheath protein, C-terminal domain / Phage tail sheath C-terminal domain / identical protein binding / Similar to FI genes of P2, phiCTX, and PS17: tail sheath
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsGe P / Scholl D / Leiman PG / Yu X / Miller JF / Zhou ZH
CitationJournal: Nat Struct Mol Biol / Year: 2015
Title: Atomic structures of a bactericidal contractile nanotube in its pre- and postcontraction states.
Authors: Peng Ge / Dean Scholl / Petr G Leiman / Xuekui Yu / Jeff F Miller / Z Hong Zhou /
Abstract: R-type pyocins are representatives of contractile ejection systems, a class of biological nanomachines that includes, among others, the bacterial type VI secretion system (T6SS) and contractile ...R-type pyocins are representatives of contractile ejection systems, a class of biological nanomachines that includes, among others, the bacterial type VI secretion system (T6SS) and contractile bacteriophage tails. We report atomic models of the Pseudomonas aeruginosa precontraction pyocin sheath and tube, and the postcontraction sheath, obtained by cryo-EM at 3.5-Å and 3.9-Å resolutions, respectively. The central channel of the tube is negatively charged, in contrast to the neutral and positive counterparts in T6SSs and phage tails. The sheath is interwoven by long N- and C-terminal extension arms emanating from each subunit, which create an extensive two-dimensional mesh that has the same connectivity in the extended and contracted state of the sheath. We propose that the contraction process draws energy from electrostatic and shape complementarities to insert the inner tube through bacterial cell membranes to eventually kill the bacteria.
History
DepositionFeb 17, 2015-
Header (metadata) releaseMar 18, 2015-
Map releaseApr 1, 2015-
UpdateMay 27, 2015-
Current statusMay 27, 2015Processing site: RCSB / Status: Released

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Structure visualization

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  • Surface view with section colored by density value
  • Surface level: 0.04
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  • Surface view colored by cylindrical radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j9r
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j9r
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3j9r
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_6271.gif

Downloads & links

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Map

FileDownload / File: emd_6271.map.gz / Format: CCP4 / Size: 100.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPyocin, contracted sheath
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 300 pix.
= 331.2 Å		1.1 Å/pix.
x 300 pix.
= 331.2 Å		1.1 Å/pix.
x 300 pix.
= 331.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.104 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.13642333 - 0.18895672
Average (Standard dev.)0.00169625 (±0.01684236)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-150-150-150
Dimensions300300300
Spacing300300300
CellA=B=C: 331.19998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1041.1041.104
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z331.200331.200331.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-72-72-72
NX/NY/NZ145145145
MAP C/R/S123
start NC/NR/NS-150-150-150
NC/NR/NS300300300
D min/max/mean-0.1360.1890.002

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Supplemental data

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Sample components

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Entire : Pyocin (post-contraction)

EntireName: Pyocin (post-contraction)
Components
  • Sample: Pyocin (post-contraction)
  • Protein or peptide: pyocin tail sheath

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Supramolecule #1000: Pyocin (post-contraction)

SupramoleculeName: Pyocin (post-contraction) / type: sample / ID: 1000 / Oligomeric state: helical / Number unique components: 1

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Macromolecule #1: pyocin tail sheath

MacromoleculeName: pyocin tail sheath / type: protein_or_peptide / ID: 1 / Name.synonym: sheath / Oligomeric state: helix of hexameric rings / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Pseudomonas aeruginosa (bacteria) / Strain: PAO
SequenceUniProtKB: Similar to FI genes of P2, phiCTX, and PS17: tail sheath

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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

BufferpH: 7.4 / Details: 1x PBS
GridDetails: baked 1.2/1.3 Quantifoil
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 90 K / Instrument: FEI VITROBOT MARK IV / Method: blot time 4 seconds, blot force 1

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureAverage: 80 K
DetailsScanned with 9200 ED
DateOct 7, 2009
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.35 µm / Number real images: 307 / Average electron dose: 25 e/Å2 / Bits/pixel: 16
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.6 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsRelion-based IHRSR
Final reconstructionApplied symmetry - Helical parameters - Δz: 16.2 Å
Applied symmetry - Helical parameters - Δ&Phi: 33.1 °
Applied symmetry - Helical parameters - Axial symmetry: C6 (6 fold cyclic)
Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: OTHER / Software - Name: Relion, IHRSR
CTF correctionDetails: Each particle

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