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- EMDB-1100: Structural insights into the assembly of the type III secretion n... -

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Basic information

Entry
Database: EMDB / ID: EMD-1100
TitleStructural insights into the assembly of the type III secretion needle complex.
Map datanone
Sample
  • Sample: Needle Complex of the Type III Secretion from Salmonella typhimurium
  • Protein or peptide: PrgH
  • Protein or peptide: PrgK
  • Protein or peptide: InvG
  • Protein or peptide: PrgJ
  • Protein or peptide: PRGI
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria) / Salmonella tyhpimurium
Methodsingle particle reconstruction / cryo EM / Resolution: 17.0 Å
AuthorsMarlovits TC / Kubori T / Sukhan A / Thomas DR / Galan JE / Unger VM
CitationJournal: Science / Year: 2004
Title: Structural insights into the assembly of the type III secretion needle complex.
Authors: Thomas C Marlovits / Tomoko Kubori / Anand Sukhan / Dennis R Thomas / Jorge E Galán / Vinzenz M Unger /
Abstract: Type III secretion systems (TTSSs) mediate translocation of virulence factors into host cells. We report the 17-angstrom resolution structures of a central component of Salmonella typhimurium TTSS, ...Type III secretion systems (TTSSs) mediate translocation of virulence factors into host cells. We report the 17-angstrom resolution structures of a central component of Salmonella typhimurium TTSS, the needle complex, and its assembly precursor, the bacterial envelope-anchored base. Both the base and the fully assembled needle complex adopted multiple oligomeric states in vivo, and needle assembly was accompanied by recruitment of the protein PrgJ as a structural component of the base. Moreover, conformational changes during needle assembly created scaffolds for anchoring both PrgJ and the needle substructure and may provide the basis for substrate-specificity switching during type III secretion.
History
DepositionSep 28, 2004-
Header (metadata) releaseOct 21, 2004-
Map releaseDec 21, 2004-
UpdateOct 17, 2012-
Current statusOct 17, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.050322561
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.050322561
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1100.gif

Downloads & links

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Map

FileDownload / File: emd_1100.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationnone
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.8 Å/pix.
x 200 pix.
= 560. Å		2.8 Å/pix.
x 200 pix.
= 560. Å		2.8 Å/pix.
x 200 pix.
= 560. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.8 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.0227 / Movie #1: 0.0503226
Minimum - Maximum-0.198282 - 0.318236
Average (Standard dev.)0.000171837 (±0.022488)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 560 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.82.82.8
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z560.000560.000560.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-32-32-32
NX/NY/NZ646464
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.1980.3180.000

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Supplemental data

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Sample components

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Entire : Needle Complex of the Type III Secretion from Salmonella typhimurium

EntireName: Needle Complex of the Type III Secretion from Salmonella typhimurium
Components
  • Sample: Needle Complex of the Type III Secretion from Salmonella typhimurium
  • Protein or peptide: PrgH
  • Protein or peptide: PrgK
  • Protein or peptide: InvG
  • Protein or peptide: PrgJ
  • Protein or peptide: PRGI

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Supramolecule #1000: Needle Complex of the Type III Secretion from Salmonella typhimurium

SupramoleculeName: Needle Complex of the Type III Secretion from Salmonella typhimurium
type: sample / ID: 1000
Details: theoretical molecular weight for the base (without the needle filament and the inner rod) is approximately 2.7MDa
Oligomeric state: 20 / Number unique components: 5

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Macromolecule #1: PrgH

MacromoleculeName: PrgH / type: protein_or_peptide / ID: 1 / Recombinant expression: No
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)

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Macromolecule #2: PrgK

MacromoleculeName: PrgK / type: protein_or_peptide / ID: 2 / Recombinant expression: No
Source (natural)Organism: Salmonella tyhpimurium
Molecular weightExperimental: 28 MDa

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Macromolecule #3: InvG

MacromoleculeName: InvG / type: protein_or_peptide / ID: 3 / Recombinant expression: No
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Molecular weightExperimental: 60 MDa

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Macromolecule #4: PrgJ

MacromoleculeName: PrgJ / type: protein_or_peptide / ID: 4 / Recombinant expression: No
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Molecular weightExperimental: 10 MDa

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Macromolecule #5: PRGI

MacromoleculeName: PRGI / type: protein_or_peptide / ID: 5 / Recombinant expression: No
Source (natural)Organism: Salmonella tyhpimurium
Molecular weightExperimental: 8 MDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8 / Details: 10mM Tris-HCl 500mM NaCl 0.2% LDAO
GridDetails: 400 mesh Cu/Rh grid
VitrificationCryogen name: ETHANE / Details: Vitrification carried out in the cold room / Method: Blot for 15 seconds before plunging

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Electron microscopy

MicroscopeFEI TECNAI F20
TemperatureAverage: 95 K
Alignment procedureLegacy - Astigmatism: 220,000
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 79 / Average electron dose: 10 e/Å2 / Od range: 0.8 / Bits/pixel: 8
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.3 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder
Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

DetailsThe particles were selected interactively at the computer terminal.
CTF correctionDetails: phase flipping, each particle
Final reconstructionApplied symmetry - Point group: C20 (20 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 17.0 Å / Resolution method: OTHER / Software - Name: SPIDER, IMAGIC, MRC / Details: supervised projection matching procedure / Number images used: 1391

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