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- EMDB-1214: Assembly of the inner rod determines needle length in the type II... -

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Basic information

Entry
Database: EMDB / ID: EMD-1214
TitleAssembly of the inner rod determines needle length in the type III secretion injectisome.
Map dataType III Secretion Complex from an invJ-mutant strainType three secretion system
Sample
  • Sample: Type III Secretion Complex from an invJ-mutant strain of Salmonella typhimuriumType three secretion system
  • Protein or peptide: PrgH
  • Protein or peptide: PrgK
  • Protein or peptide: InvG
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 20.0 Å
AuthorsMarlovits TC / Kubori T / Lara-Tejero M / Thomas D / Unger VM / Galan JE
CitationJournal: Nature / Year: 2006
Title: Assembly of the inner rod determines needle length in the type III secretion injectisome.
Authors: Thomas C Marlovits / Tomoko Kubori / María Lara-Tejero / Dennis Thomas / Vinzenz M Unger / Jorge E Galán /
Abstract: Assembly of multi-component supramolecular machines is fundamental to biology, yet in most cases, assembly pathways and their control are poorly understood. An example is the type III secretion ...Assembly of multi-component supramolecular machines is fundamental to biology, yet in most cases, assembly pathways and their control are poorly understood. An example is the type III secretion machine, which mediates the transfer of bacterial virulence proteins into host cells. A central component of this nanomachine is the needle complex or injectisome, an organelle associated with the bacterial envelope that is composed of a multi-ring base, an inner rod, and a protruding needle. Assembly of this organelle proceeds in sequential steps that require the reprogramming of the secretion machine. Here we provide evidence that, in Salmonella typhimurium, completion of the assembly of the inner rod determines the size of the needle substructure. Assembly of the inner rod, which is regulated by the InvJ protein, triggers conformational changes on the cytoplasmic side of the injectisome, reprogramming the secretion apparatus to stop secretion of the needle protein.
History
DepositionApr 13, 2006-
Header (metadata) releaseApr 13, 2006-
Map releaseJul 28, 2006-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.07
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1214.gif

Downloads & links

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Map

FileDownload / File: emd_1214.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationType III Secretion Complex from an invJ-mutant strain
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: 0.0577 / Movie #1: 0.07
Minimum - Maximum-0.299914 - 0.640356
Average (Standard dev.)0.000851163 (±0.0379139)
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-96-96-96
NX/NY/NZ192192192
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.3000.6400.001

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Supplemental data

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Sample components

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Entire : Type III Secretion Complex from an invJ-mutant strain of Salmonel...

EntireName: Type III Secretion Complex from an invJ-mutant strain of Salmonella typhimuriumType three secretion system
Components
  • Sample: Type III Secretion Complex from an invJ-mutant strain of Salmonella typhimuriumType three secretion system
  • Protein or peptide: PrgH
  • Protein or peptide: PrgK
  • Protein or peptide: InvG

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Supramolecule #1000: Type III Secretion Complex from an invJ-mutant strain of Salmonel...

SupramoleculeName: Type III Secretion Complex from an invJ-mutant strain of Salmonella typhimurium
type: sample / ID: 1000 / Oligomeric state: 20 / Number unique components: 3
Molecular weightTheoretical: 2.64 MDa

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Macromolecule #1: PrgH

MacromoleculeName: PrgH / type: protein_or_peptide / ID: 1 / Number of copies: 20 / Recombinant expression: Yes
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
synonym: Salmonella / Location in cell: Membrane
Molecular weightExperimental: 44 MDa
Recombinant expressionOrganism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)

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Macromolecule #2: PrgK

MacromoleculeName: PrgK / type: protein_or_peptide / ID: 2 / Number of copies: 20 / Recombinant expression: Yes
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
synonym: Salmonella / Location in cell: Membrane
Molecular weightExperimental: 28 MDa
Recombinant expressionOrganism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)

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Macromolecule #3: InvG

MacromoleculeName: InvG / type: protein_or_peptide / ID: 3 / Number of copies: 20 / Recombinant expression: Yes
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
synonym: Salmonella / Location in cell: Membrane
Molecular weightExperimental: 60 MDa
Recombinant expressionOrganism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)

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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
VitrificationCryogen name: ETHANE / Method: Blot for 15 seconds before plunging

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 4.2 µm / Nominal defocus min: 1.7 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Side-entry liquid nitrogen-cooled cryo specimen holder
Specimen holder model: GATAN LIQUID NITROGEN
Alignment procedureLegacy - Astigmatism: 200
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 61 / Average electron dose: 10 e/Å2 / Od range: 0.8 / Bits/pixel: 8
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: phase flipping, each particle
Final reconstructionApplied symmetry - Point group: C20 (20 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER, IMAGIC-5, MRC / Details: supervised projection matching procedure

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