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- EMDB-6266: CryoEM structure of a type VI secretion system -

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Basic information

Entry
Database: EMDB / ID: EMD-6266
TitleCryoEM structure of a type VI secretion system
Map dataContracted T6SS sheath
Sample
  • Sample: Contracted T6SS sheath
  • Protein or peptide: IglA
  • Protein or peptide: IglB
KeywordsT6SS / Francisella tularensis subsp. novicida
Function / homology
Function and homology information


host cell cytoplasm
Similarity search - Function
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
Intracellular growth locus protein B / Intracellular growth locus protein A
Similarity search - Component
Biological speciesFrancisella novicida U112 (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsClemens DL / Ge P / Lee BY / Horwitz MA / Zhou ZH
CitationJournal: Cell / Year: 2015
Title: Atomic structure of T6SS reveals interlaced array essential to function.
Authors: Daniel L Clemens / Peng Ge / Bai-Yu Lee / Marcus A Horwitz / Z Hong Zhou /
Abstract: Type VI secretion systems (T6SSs) are newly identified contractile nanomachines that translocate effector proteins across bacterial membranes. The Francisella pathogenicity island, required for ...Type VI secretion systems (T6SSs) are newly identified contractile nanomachines that translocate effector proteins across bacterial membranes. The Francisella pathogenicity island, required for bacterial phagosome escape, intracellular replication, and virulence, was presumed to encode a T6SS-like apparatus. Here, we experimentally confirm the identity of this T6SS and, by cryo electron microscopy (cryoEM), show the structure of its post-contraction sheath at 3.7 Å resolution. We demonstrate the assembly of this T6SS by IglA/IglB and secretion of its putative effector proteins in response to environmental stimuli. The sheath has a quaternary structure with handedness opposite that of contracted sheath of T4 phage tail and is organized in an interlaced two-dimensional array by means of β sheet augmentation. By structure-based mutagenesis, we show that this interlacing is essential to secretion, phagosomal escape, and intracellular replication. Our atomic model of the T6SS will facilitate design of drugs targeting this highly prevalent secretion apparatus.
History
DepositionFeb 11, 2015-
Header (metadata) releaseMar 18, 2015-
Map releaseMar 18, 2015-
UpdateMar 18, 2015-
Current statusMar 18, 2015Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.017
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.017
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j9o
  • Surface level: 0.017
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j9o
  • Surface level: 0.017
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3j9o
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_6266.gif

Downloads & links

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Map

FileDownload / File: emd_6266.map.gz / Format: CCP4 / Size: 122.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationContracted T6SS sheath
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 320 pix.
= 320. Å		1 Å/pix.
x 320 pix.
= 320. Å		1 Å/pix.
x 320 pix.
= 320. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.017 / Movie #1: 0.017
Minimum - Maximum-0.0385328 - 0.06183224
Average (Standard dev.)0.00024367 (±0.00821327)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-160-160-160
Dimensions320320320
Spacing320320320
CellA=B=C: 320.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z111
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z320.000320.000320.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-72-72-72
NX/NY/NZ145145145
MAP C/R/S123
start NC/NR/NS-160-160-160
NC/NR/NS320320320
D min/max/mean-0.0390.0620.000

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Supplemental data

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Sample components

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Entire : Contracted T6SS sheath

EntireName: Contracted T6SS sheath
Components
  • Sample: Contracted T6SS sheath
  • Protein or peptide: IglA
  • Protein or peptide: IglB

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Supramolecule #1000: Contracted T6SS sheath

SupramoleculeName: Contracted T6SS sheath / type: sample / ID: 1000 / Oligomeric state: Helix of IglA/IglB dimers / Number unique components: 2

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Macromolecule #1: IglA

MacromoleculeName: IglA / type: protein_or_peptide / ID: 1 / Name.synonym: T6SS sheath / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Francisella novicida U112 (bacteria)
SequenceUniProtKB: Intracellular growth locus protein A

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Macromolecule #2: IglB

MacromoleculeName: IglB / type: protein_or_peptide / ID: 2 / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Francisella novicida U112 (bacteria)
SequenceUniProtKB: Intracellular growth locus protein B

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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: 7.5 / Details: 20 mM Tris, 0.9% NaCl
GridDetails: 200 mesh Quantifoil 1.2/1.3
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 90 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureAverage: 80 K
Alignment procedureLegacy - Astigmatism: Software
DetailsK2 Summit in Counting mode
DateMar 1, 2014
Image recordingCategory: CCD / Film or detector model: GATAN K2 (4k x 4k) / Number real images: 1644 / Average electron dose: 25 e/Å2 / Details: 480,000 asymmetric units
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: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 29000
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: 20.8 Å
Applied symmetry - Helical parameters - Δ&Phi: 33.4 °
Applied symmetry - Helical parameters - Axial symmetry: C6 (6 fold cyclic)
Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: OTHER / Software - Name: Relion, IHRSR
CTF correctionDetails: each particle

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