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- EMDB-3216: In situ sub-tomogram average of the host-free Chlamydia trachomat... -

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Basic information

Entry
Database: EMDB / ID: EMD-3216
TitleIn situ sub-tomogram average of the host-free Chlamydia trachomatis type III secretion systemType three secretion system
Map dataSub-tomogram average of Chlamydia type III secretion system (host-free)Type three secretion system
Sample
  • Sample: Chlamydia trachomatis type III secretion system (host-free)Type three secretion system
  • Organelle or cellular component: Chlamydia trachomatis type III secretion system (host-free)Type three secretion system
Keywordsinjectisome / type III secretion / T3SS
Biological speciesChlamydia trachomatis (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 33.0 Å
AuthorsNans A / Kudryashev M / Saibil HR / Hayward RD
CitationJournal: Nat Commun / Year: 2015
Title: Structure of a bacterial type III secretion system in contact with a host membrane in situ.
Authors: Andrea Nans / Mikhail Kudryashev / Helen R Saibil / Richard D Hayward /
Abstract: Many bacterial pathogens of animals and plants use a conserved type III secretion system (T3SS) to inject virulence effector proteins directly into eukaryotic cells to subvert host functions. Contact ...Many bacterial pathogens of animals and plants use a conserved type III secretion system (T3SS) to inject virulence effector proteins directly into eukaryotic cells to subvert host functions. Contact with host membranes is critical for T3SS activation, yet little is known about T3SS architecture in this state or the conformational changes that drive effector translocation. Here we use cryo-electron tomography and sub-tomogram averaging to derive the intact structure of the primordial Chlamydia trachomatis T3SS in the presence and absence of host membrane contact. Comparison of the averaged structures demonstrates a marked compaction of the basal body (4 nm) occurs when the needle tip contacts the host cell membrane. This compaction is coupled to a stabilization of the cytosolic sorting platform-ATPase. Our findings reveal the first structure of a bacterial T3SS from a major human pathogen engaged with a eukaryotic host, and reveal striking 'pump-action' conformational changes that underpin effector injection.
History
DepositionOct 26, 2015-
Header (metadata) releaseNov 18, 2015-
Map releaseDec 16, 2015-
UpdateDec 30, 2015-
Current statusDec 30, 2015Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.74
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 3.74
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-3216_sna...

Downloads & links

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Map

FileDownload / File: emd_3216.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSub-tomogram average of Chlamydia type III secretion system (host-free)
Voxel sizeX=Y=Z: 5.4 Å
Density
Contour LevelBy AUTHOR: 3.74 / Movie #1: 3.74
Minimum - Maximum0.0 - 7.11611032
Average (Standard dev.)3.14649796 (±0.24851274)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 1382.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.45.45.4
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z1382.4001382.4001382.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-300-64
NX/NY/NZ6161129
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean0.0007.1163.146

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Supplemental data

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Supplemental map: Subtomo EMD-3216.map

FileSubtomo_EMD-3216.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Chlamydia trachomatis type III secretion system (host-free)

EntireName: Chlamydia trachomatis type III secretion system (host-free)Type three secretion system
Components
  • Sample: Chlamydia trachomatis type III secretion system (host-free)Type three secretion system
  • Organelle or cellular component: Chlamydia trachomatis type III secretion system (host-free)Type three secretion system

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Supramolecule #1000: Chlamydia trachomatis type III secretion system (host-free)

SupramoleculeName: Chlamydia trachomatis type III secretion system (host-free)
type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Chlamydia trachomatis type III secretion system (host-free)

SupramoleculeName: Chlamydia trachomatis type III secretion system (host-free)
type: organelle_or_cellular_component / ID: 1 / Recombinant expression: No
Source (natural)Organism: Chlamydia trachomatis (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

GridDetails: 200 mesh gold quantifoil grid 3.5/1
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV / Method: Blot for 2.5 seconds

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Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.3 mm / Nominal defocus max: -10.0 µm / Nominal magnification: 41000
Specialist opticsEnergy filter - Name: Gatan Quantum / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC / Tilt series - Axis1 - Min angle: -45 ° / Tilt series - Axis1 - Max angle: 60 °
DateSep 1, 2014
Image recordingCategory: CCD / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 55 e/Å2
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each micrograph was phase-flipped in IMOD according to the measured defocus.
Final reconstructionApplied symmetry - Point group: C12 (12 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 33.0 Å / Resolution method: OTHER / Software - Name: IMOD, Dynamo / Number subtomograms used: 515
DetailsSub-tomograms selected in IMOD and cropped with Dynamo. Alignment and averaging was done in Dynamo.

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