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- EMDB-1416: Helical structure of the needle of the type III secretion system ... -

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Basic information

Entry
Database: EMDB / ID: EMD-1416
TitleHelical structure of the needle of the type III secretion system of Shigella flexneri.
Map dataccp4 map of reconstruction of Shigella flexneri T3SS needle
Sample
  • Sample: Shigella flexneri T3SS needle - MxiH polymer
  • Protein or peptide: MxiH
Function / homology
Function and homology information


type III protein secretion system complex / protein secretion by the type III secretion system / cell surface / extracellular region / identical protein binding
Similarity search - Function
Type III secretion, needle-protein-like / Type III secretion, needle-protein-like superfamily / Type III secretion needle MxiH, YscF, SsaG, EprI, PscF, EscF / Type III secretion system, needle protein / Type III secretion system, needle protein
Similarity search - Domain/homology
Type 3 secretion system needle filament protein
Similarity search - Component
Biological speciesShigella flexneri (bacteria)
Methodhelical reconstruction / cryo EM / negative staining / Resolution: 16.0 Å
AuthorsCordes FS / Komoriya K / Larquet E / Yang S / Egelman EH / Blocker A / Lea SM
CitationJournal: J Biol Chem / Year: 2003
Title: Helical structure of the needle of the type III secretion system of Shigella flexneri.
Authors: Frank S Cordes / Kaoru Komoriya / Eric Larquet / Shixin Yang / Edward H Egelman / Ariel Blocker / Susan M Lea /
Abstract: Gram-negative bacteria commonly interact with animal and plant hosts using type III secretion systems (TTSSs) for translocation of proteins into eukaryotic cells during infection. 10 of the 25 TTSS- ...Gram-negative bacteria commonly interact with animal and plant hosts using type III secretion systems (TTSSs) for translocation of proteins into eukaryotic cells during infection. 10 of the 25 TTSS-encoding genes are homologous to components of the bacterial flagellar basal body, which the TTSS needle complex morphologically resembles. This indicates a common ancestry, although no TTSS sequence homologues for the genes encoding the flagellum are found. We here present an approximately 16-A structure of the central component, the needle, of the TTSS. Although the needle subunit is significantly smaller and shares no sequence homology with the flagellar hook and filament, it shares a common helical architecture ( approximately 5.6 subunits/turn, 24-A helical pitch). This common architecture implies that there will be further mechanistic analogies in the functioning of these two bacterial systems.
History
DepositionAug 31, 2007-
Header (metadata) releaseAug 31, 2007-
Map releaseAug 31, 2007-
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: 130
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 130
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-2v6l
  • Surface level: 130
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-2v6l
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1416.gif

Downloads & links

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Map

FileDownload / File: emd_1416.map.gz / Format: CCP4 / Size: 1.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationccp4 map of reconstruction of Shigella flexneri T3SS needle
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
2.65 Å/pix.
x 100 pix.
= 265. Å		2.65 Å/pix.
x 60 pix.
= 159. Å		2.65 Å/pix.
x 60 pix.
= 159. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 2.65 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 221.0 / Movie #1: 130
Minimum - Maximum-66.356999999999999 - 560.347999999999956
Average (Standard dev.)28.020900000000001 (±79.573999999999998)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-30-30-49
Dimensions6060100
Spacing6060100
CellA: 159 Å / B: 159 Å / C: 265 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.652.652.65
M x/y/z6060100
origin x/y/z0.0000.0000.000
length x/y/z159.000159.000265.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-30-30-49
NX/NY/NZ6060100
MAP C/R/S213
start NC/NR/NS-30-30-49
NC/NR/NS6060100
D min/max/mean-66.357560.34828.021

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Supplemental data

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Sample components

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Entire : Shigella flexneri T3SS needle - MxiH polymer

EntireName: Shigella flexneri T3SS needle - MxiH polymer
Components
  • Sample: Shigella flexneri T3SS needle - MxiH polymer
  • Protein or peptide: MxiH

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Supramolecule #1000: Shigella flexneri T3SS needle - MxiH polymer

SupramoleculeName: Shigella flexneri T3SS needle - MxiH polymer / type: sample / ID: 1000 / Oligomeric state: helical / Number unique components: 1

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Macromolecule #1: MxiH

MacromoleculeName: MxiH / type: protein_or_peptide / ID: 1 / Name.synonym: MxiH / Oligomeric state: helical polymer / Recombinant expression: Yes
Source (natural)Organism: Shigella flexneri (bacteria) / Strain: M90T / Location in cell: extracellular
Molecular weightExperimental: 9265 MDa
Recombinant expressionOrganism: Shigella flexneri (bacteria) / Recombinant plasmid: pKT001
SequenceInterPro: Type III secretion system, needle protein

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration0.1 mg/mL
BufferpH: 7.5 / Details: 10mM Tris pH 7.5
StainingType: NEGATIVE / Details: 2% uranyl acetate, pH 7.5
GridDetails: 200 mesh carbon coated copper
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI/PHILIPS CM120T
TemperatureAverage: 293 K
Detailslow dose conditions
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Number real images: 18 / Average electron dose: 10 e/Å2 / Details: 1600dpi, 2.65 Angstrom per pixel
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 0.7 µm / Nominal defocus min: 0.7 µm / Nominal magnification: 60000
Sample stageSpecimen holder: Eucentric / Specimen holder model: OTHER

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Image processing

Detailsthe 5-start helix is left handed
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 16.0 Å / Resolution method: OTHER / Software - Name: SPIDER and MRC / Details: see paper

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Atomic model buiding 1

Initial modelPDB ID:

2ca5

SoftwareName: BUSTER-TnT
DetailsProtocol: Rigid Body. Fitted by hand and optimised using URO. Helical parameters used.
RefinementSpace: RECIPROCAL / Protocol: RIGID BODY FIT / Overall B value: 50 / Target criteria: Correlation Coefficient and R_factor
Output model

PDB-2v6l:
Molecular Model of a Type III Secretion System Needle

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