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- PDB-5urx: Structure of the contracted type VI secretion system sheath in My... -

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Basic information

Entry
Database: PDB / ID: 5urx
TitleStructure of the contracted type VI secretion system sheath in Myxococcus xanthus
Components
  • TssB
  • TssC
KeywordsPROTEIN TRANSPORT / T6SS / type IV secretion / protein machine / secretion system / sheath / contractile
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 / Uncharacterized protein / Uncharacterized protein
Function and homology information
Specimen sourceMyxococcus xanthus (bacteria)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / 28 Å resolution
AuthorsChang, Y.-W. / Rettberg, L.A. / Jensen, G.J.
CitationJournal: EMBO Rep. / Year: 2017
Title: structures of an intact type VI secretion system revealed by electron cryotomography.
Authors: Yi-Wei Chang / Lee A Rettberg / Davi R Ortega / Grant J Jensen
Abstract: The type VI secretion system (T6SS) is a versatile molecular weapon used by many bacteria against eukaryotic hosts or prokaryotic competitors. It consists of a cytoplasmic bacteriophage tail-like ...The type VI secretion system (T6SS) is a versatile molecular weapon used by many bacteria against eukaryotic hosts or prokaryotic competitors. It consists of a cytoplasmic bacteriophage tail-like structure anchored in the bacterial cell envelope via a cytoplasmic baseplate and a periplasmic membrane complex. Rapid contraction of the sheath in the bacteriophage tail-like structure propels an inner tube/spike complex through the target cell envelope to deliver effectors. While structures of purified contracted sheath and purified membrane complex have been solved, because sheaths contract upon cell lysis and purification, no structure is available for the extended sheath. Structural information about the baseplate is also lacking. Here, we use electron cryotomography to directly visualize intact T6SS structures inside cells. Using sub-tomogram averaging, we resolve the structure of the extended sheath and membrane-associated components including the baseplate. Moreover, we identify novel extracellular bacteriophage tail fiber-like antennae. These results provide new structural insights into how the extended sheath prevents premature disassembly and how this sophisticated machine may recognize targets.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 13, 2017 / Release: May 10, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0May 10, 2017Structure modelrepositoryInitial release
1.1May 24, 2017Structure modelDatabase references
1.2Jul 12, 2017Structure modelDatabase referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
1A: TssB
1B: TssC
1C: TssB
1D: TssC
1E: TssB
1F: TssC
1G: TssB
1H: TssC
1I: TssB
1J: TssC
1K: TssB
1L: TssC
2A: TssB
2B: TssC
2C: TssB
2D: TssC
2E: TssB
2F: TssC
2G: TssB
2H: TssC
2I: TssB
2J: TssC
2K: TssB
2L: TssC
3A: TssB
3B: TssC
3C: TssB
3D: TssC
3E: TssB
3F: TssC
3G: TssB
3H: TssC
3I: TssB
3J: TssC
3K: TssB
3L: TssC


Theoretical massNumber of molelcules
Total (without water)1,335,69236
Polyers1,335,69236
Non-polymers00
Water0
1


  • idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein/peptide
TssB


Mass: 18016.617 Da / Num. of mol.: 18 / Source: (natural) Myxococcus xanthus (bacteria) / Strain: DK 1622 / References: UniProt: Q1D305
#2: Protein/peptide
TssC


Mass: 56188.469 Da / Num. of mol.: 18 / Source: (natural) Myxococcus xanthus (bacteria) / Strain: DK 1622 / References: UniProt: Q1D304

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: CELL / Reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: Type VI secretion system / Type: COMPLEX / Entity ID: 1, 2 / Source: NATURAL
Source (natural)Organism: Myxococcus xanthus DK 1622 (bacteria)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 1.5 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameCategory
2UCSFTomoimage acquisition
4IMODCTF correction
11PEETfinal Euler assignment
12PEETclassification
13Tomo3d3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 28 Å / Resolution method: OTHER / Number of particles: 407 / Symmetry type: POINT
EM volume selectionNumber of tomograms: 24 / Number of volumes extracted: 407

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