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- EMDB-8602: Sub-tomogram average of the contracted type VI secretion system s... -

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Basic information

Entry
Database: EMDB / ID: EMD-8602
TitleSub-tomogram average of the contracted type VI secretion system sheath in Myxococcus xanthus
Map data
Sample
  • Complex: Type VI secretion system
    • Protein or peptide: TssB
    • Protein or peptide: TssC
KeywordsT6SS / type IV secretion / protein machine / secretion system / sheath / contractile / PROTEIN TRANSPORT
Function / homologyType 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 / Type VI secretion protein / Type VI secretion system-associated protein
Function and homology information
Biological speciesMyxococcus xanthus DK 1622 (bacteria) / Myxococcus xanthus (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 28.0 Å
AuthorsChang Y-W / Rettberg LA / Jensen GJ
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.
History
DepositionFeb 13, 2017-
Header (metadata) releaseMar 22, 2017-
Map releaseMay 10, 2017-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 39800
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 39800
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5urx
  • Surface level: 39800
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5urx
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8602.png

Downloads & links

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Map

FileDownload / File: emd_8602.map.gz / Format: CCP4 / Size: 844.7 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
7.8 Å/pix.
x 60 pix.
= 468. Å		7.8 Å/pix.
x 60 pix.
= 468. Å		7.8 Å/pix.
x 60 pix.
= 468. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 7.8 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 39800.0 / Movie #1: 39800
Minimum - Maximum0.0009765625 - 65535.0
Average (Standard dev.)32553.326000000000931 (±8674.891999999999825)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions606060
Spacing606060
CellA: 468.00003 Å / B: 468.0 Å / C: 468.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z7.87.87.8
M x/y/z606060
origin x/y/z0.0000.0000.000
length x/y/z468.000468.000468.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS606060
D min/max/mean0.00165535.00032553.326

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Supplemental data

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Sample components

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Entire : Type VI secretion system

EntireName: Type VI secretion system
Components
  • Complex: Type VI secretion system
    • Protein or peptide: TssB
    • Protein or peptide: TssC

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Supramolecule #1: Type VI secretion system

SupramoleculeName: Type VI secretion system / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Myxococcus xanthus DK 1622 (bacteria)

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Macromolecule #1: TssB

MacromoleculeName: TssB / type: protein_or_peptide / ID: 1 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Myxococcus xanthus (bacteria) / Strain: DK 1622
Molecular weightTheoretical: 18.016617 KDa
SequenceString:
MSKESSVAPT ERVNIVYKPA TGNAQEQVEL PLKVLMLGDF TGQEDARPLE QRAPINVDKA NFNEVMAQQN LKVTLTAADK LSADPNATM NVSLQFKNLN DFSPESVVNQ VPELKKLLEL RSALNALKGP LGNLPAFRKK LQALLADEDG RKALIKELGL T EETK

UniProtKB: Type VI secretion system-associated protein

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Macromolecule #2: TssC

MacromoleculeName: TssC / type: protein_or_peptide / ID: 2 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Myxococcus xanthus (bacteria) / Strain: DK 1622
Molecular weightTheoretical: 56.188469 KDa
SequenceString: MANETQTQKS TGVANDASLS LLDEILSEAK LKPKDEGYDV AKRGVQAFIT EMLAPNRSEE RVDKALVDAM IAEIDKRLSS QVNEILHAK EFQKLESSWR SLKFMVDRTD FRENTRVEML NASKEDLQKD FEDAPEVTKS GLYKLVYSNE YGVFGGKPYG I ISANYDFN ...String:
MANETQTQKS TGVANDASLS LLDEILSEAK LKPKDEGYDV AKRGVQAFIT EMLAPNRSEE RVDKALVDAM IAEIDKRLSS QVNEILHAK EFQKLESSWR SLKFMVDRTD FRENTRVEML NASKEDLQKD FEDAPEVTKS GLYKLVYSNE YGVFGGKPYG I ISANYDFN VGPQDMELLR KCASVAAMAH APFIGNAAPE VFGEESFLKL PDLKDLKSLF EGPQYARWHS FRESEDARYV GL ALPRFLL RLPYGEKTVP VKAFNFTEDV VGHHERYLWG HASVALTSRV ADSFAKFRWS PNIIGPQSGG AVENLPLHQY EAM GEIQTK IPTEVMLTER REFELSEEGF IGLVFRKDSD NAAFFSANST QKPRFFGNTP EGKAAETNYR LGTQLPYMFI MTRL AHYIK VLQREQIGSW KEKSDLEREL NHWLSQYISD MDDPAPAVRS RRPLRAARVV VEDVEGQPGW YRCSLQVRPH FKYMG ASFT LSLVGKLDKE

UniProtKB: Type VI secretion protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / 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: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 28.0 Å / Resolution method: OTHER / Software - Name: TOMO3D / Number subtomograms used: 407
ExtractionNumber tomograms: 24 / Number images used: 407
Final 3D classificationSoftware - Name: PEET
Final angle assignmentType: OTHER / Software - Name: PEET

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