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- EMDB-1422: Structure and composition of the Shigella flexneri "needle comple... -

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Basic information

Entry
Database: EMDB / ID: 1422
TitleStructure and composition of the Shigella flexneri "needle complex", a part of its type III secreton.
Sampleneedle complex or basal body of the Shigella flexneri T3SS
SourceShigella flexneri / bacteria / シゲラ・フレクスネリ, フレクスナー赤痢菌
Map dataBasal Body of Shigella flexneri T3SS - needle removed
Methodsingle particle reconstruction, at 17 A resolution
AuthorsBlocker AJ / Jouihri N / Larquet E / Gounon P / Ebel F / Parsot C / Sansonetti P / Allaoui A
CitationMol. Microbiol., 2001, 39, 652-663

Mol. Microbiol., 2001, 39, 652-663 StrPapers
Structure and composition of the Shigella flexneri "needle complex", a part of its type III secreton.
A Blocker / N Jouihri / E Larquet / P Gounon / F Ebel / C Parsot / P Sansonetti / A Allaoui

DateDeposition: Aug 31, 2007 / Header (metadata) release: Sep 12, 2007 / Map release: Sep 12, 2007 / Last update: Aug 31, 2007

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 380
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 380
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_1422.map.gz (map file in CCP4 format, 105470 KB)
Projections & slicesSize of images:
AxesZ (Sec.)X (Row.)Y (Col.)
300 pix
2.2 A/pix
= 660. A
300 pix
2.2 A/pix
= 660. A
300 pix
2.2 A/pix
= 660. A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.2 A
Density
Contour Level:103, 380 (movie #1):
Minimum - Maximum-257.841 - 820.019
Average (Standard dev.)-12.8026 (115.599)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderYXZ
Dimensions300300300
Origin-150-150-149
Limit149149150
Spacing300300300
CellA=B=C: 660 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z2.22.22.2
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z660.000660.000660.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-150-150-149
NX/NY/NZ300300300
MAP C/R/S213
start NC/NR/NS-150-150-149
NC/NR/NS300300300
D min/max/mean-257.841820.019-12.803

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Supplemental data

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Sample components

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Entire needle complex or basal body of the Shigella flexneri T3SS

EntireName: needle complex or basal body of the Shigella flexneri T3SS
Oligomeric State: not yet fully determined / Number of components: 5

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Component #1: protein, MxiH

ProteinName: MxiH / Oligomeric Details: helical polymer / Details: none; copy number is approximative / Number of Copies: 120 / Recombinant expression: No
MassTheoretical: 9.265 MDa / Experimental: 9.265 MDa
SourceSpecies: Shigella flexneri / bacteria / シゲラ・フレクスネリ, フレクスナー赤痢菌
Strain: M90T
Source (natural)Organelle: T3SS / Location in cell: extracellular / Organ or tissue: bacterium
External referencesInterPro: InterPro: 011841

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Component #2: protein, MxiI

ProteinName: MxiI / Oligomeric Details: probably helical / Details: none; Copy number is approximative / Recombinant expression: No / Number of Copies: 20
MassTheoretical: 10.633 MDa / Experimental: 10.633 MDa
SourceSpecies: Shigella flexneri / bacteria / シゲラ・フレクスネリ, フレクスナー赤痢菌
Strain: M90T
Source (natural)Organelle: T3SS / Location in cell: periplasmic / Cell: bacterium

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Component #3: protein, MxiD

ProteinName: MxiD / Oligomeric Details: oligomer
Details: experimental weight is theoretical weight, with predicted signal sequence removed; oligomeric state currently unknown
Recombinant expression: No
MassTheoretical: 60.749 MDa / Experimental: 63.218 MDa
SourceSpecies: Shigella flexneri / bacteria / シゲラ・フレクスネリ, フレクスナー赤痢菌
Strain: M90T
Source (natural)Organelle: T3SS / Location in cell: outer membrane / Cell: bacterium
External referencesInterPro: InterPro: 003522 / Gene Ontology: GO: 0015448

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Component #4: protein, MxiG

ProteinName: MxiG / Oligomeric Details: oligomer
Details: no signal sequence cleavage in this protein; oligomeric state unknown
Recombinant expression: No
MassTheoretical: 43.002 MDa / Experimental: 43.002 MDa
SourceSpecies: Shigella flexneri / bacteria / シゲラ・フレクスネリ, フレクスナー赤痢菌
Strain: M90T
Source (natural)Organelle: T3SS / Location in cell: inner membrane / Cell: bacterium
External referencesGene Ontology: GO: 0005515

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Component #5: protein, MxiJ

ProteinName: MxiJ / Oligomeric Details: oligomer
Details: experimental weight is theoretical weight, with predicted signal sequence removed; oligomeric state unknown
Recombinant expression: No
MassTheoretical: 25.488 MDa / Experimental: 27.509 MDa
SourceSpecies: Shigella flexneri / bacteria / シゲラ・フレクスネリ, フレクスナー赤痢菌
Strain: M90T
Source (natural)Organelle: T3SS / Location in cell: inner membrane / Cell: bacterium
External referencesGene Ontology: GO: 0005515 / InterPro: InterPro: 006182

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionBuffer solution: samples made in 50 mM Tris pH 8, 5 mM EDTA, 0.1 % v/v Triton X-100 and diluted 1:5 in 20 mM Tris pH 7.4
pH: 7.4
Support filmcarbon-coated glow-discharged copper grids
Staining1% uranyl acetate pH 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

ImagingMicroscope: FEI/PHILIPS CM120T / Details: low-dose mode used, imaging done in 1999-2000
Electron gunElectron source: LAB6 / Accelerating voltage: 100 kV / Electron dose: 10 e/A2 / Illumination mode: SPOT SCAN
LensMagnification: 45000 X (nominal) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 600 - 1200 nm
Specimen HolderHolder: Eucentric / Model: OTHER / Temperature: 293 K ( 293 - 293 K)
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 20 / Scanner: OTHER / Sampling size: 10 microns
Details: Hi-Scan rotary drum microdensitometer used, final resolution was 2.2 A/pixel (not 5 A/ pixel as incorrectly stated in Materials and Methods of paper)

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Image processing

ProcessingMethod: single particle reconstruction / Number of class averages: 5 / Number of projections: 868
Details: Particles selected using interactive WEB selection program
3D reconstructionAlgorithm: single particle / Software: SPIDER / Resolution: 17 A
Resolution method: Fourier ring correlation and differential phase residual
Details: 1) 2D-average>iterative multireference alignment process (Boekema et al, 1986), using Ward's merging criterion until stable classes obtained; 2) 3D reconstruction> cylindrical symmetry was assumed and the final two dimensional projection converted to a three-dimensional map using an iterative back projection procedure (Frank, 1996).

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