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- EMDB-7474: Subtomogram average of the cag type IV secretion system in Helico... -

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Basic information

Entry
Database: EMDB / ID: EMD-7474
TitleSubtomogram average of the cag type IV secretion system in Helicobacter pylori cells (aligning periplasmic parts)Secretion
Map dataprimary map
Sample
  • Complex: cag type IV secretion systemSecretion
Biological speciesHelicobacter pylori (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 39.0 Å
AuthorsChang Y-W / Shaffer C / Rettberg LA / Ghosal D / Jensen GJ
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI127401 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Cell Rep / Year: 2018
Title: In Vivo Structures of the Helicobacter pylori cag Type IV Secretion System.
Authors: Yi-Wei Chang / Carrie L Shaffer / Lee A Rettberg / Debnath Ghosal / Grant J Jensen /
Abstract: The type IV secretion system (T4SS) is a versatile nanomachine that translocates diverse effector molecules between microbes and into eukaryotic cells. Here, using electron cryotomography, we reveal ...The type IV secretion system (T4SS) is a versatile nanomachine that translocates diverse effector molecules between microbes and into eukaryotic cells. Here, using electron cryotomography, we reveal the molecular architecture of the Helicobacter pylori cag T4SS. Although most components are unique to H. pylori, the cag T4SS exhibits remarkable architectural similarity to other T4SSs. Our images revealed that, when H. pylori encounters host cells, the bacterium elaborates membranous tubes perforated by lateral ports. Sub-tomogram averaging of the cag T4SS machinery revealed periplasmic densities associated with the outer membrane, a central stalk, and peripheral wing-like densities. Additionally, we resolved pilus-like rod structures extending from the cag T4SS into the inner membrane, as well as densities within the cytoplasmic apparatus corresponding to a short central barrel surrounded by four longer barrels. Collectively, these studies reveal the structure of a dynamic molecular machine that evolved to function in the human gastric niche.
History
DepositionFeb 21, 2018-
Header (metadata) releaseApr 18, 2018-
Map releaseApr 18, 2018-
UpdateDec 11, 2019-
Current statusDec 11, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 115
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 115
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7474.png

Downloads & links

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Map

FileDownload / File: emd_7474.map.gz / Format: CCP4 / Size: 5.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationprimary map
Voxel sizeX=Y=Z: 7.8 Å
Density
Contour LevelBy AUTHOR: 115 / Movie #1: 115
Minimum - Maximum-0.00003051758 - 255
Average (Standard dev.)99.12418 (±47.100075)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions150100100
Spacing100150100
CellA: 780.0 Å / B: 1170.0 Å / C: 780.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z7.87.87.8
M x/y/z100150100
origin x/y/z0.0000.0000.000
length x/y/z780.0001170.000780.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-51-35-11
NX/NY/NZ11110799
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS100150100
D min/max/mean-0.000255.00099.124

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Supplemental data

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Sample components

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Entire : cag type IV secretion system

EntireName: cag type IV secretion systemSecretion
Components
  • Complex: cag type IV secretion systemSecretion

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Supramolecule #1: cag type IV secretion system

SupramoleculeName: cag type IV secretion system / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Helicobacter pylori (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

BufferpH: 7
VitrificationCryogen name: ETHANE-PROPANE

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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
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.5 e/Å2
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 55 / Number images used: 67 / Software - Name: PEET
CTF correctionSoftware - Name: IMOD
Final 3D classificationSoftware - Name: PEET
Final angle assignmentType: OTHER / Software - Name: PEET
Final reconstructionApplied symmetry - Point group: C14 (14 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 39.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: TOMO3D / Number subtomograms used: 67

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