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Structure and composition of the Shigella flexneri "needle complex", a part of its type III secreton.

by single particle reconstruction, at 17 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 380, Made by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 380, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1422
TitleStructure and composition of the Shigella flexneri "needle complex", a part of its type III secreton.
MapBasal Body of Shigella flexneri T3SS - needle removed
Sampleneedle complex or basal body of the Shigella flexneri T3SS
AuthorsBlocker AJ, Jouihri N, Larquet E, Gounon P, Ebel F, Parsot C, Sansonetti P, Allaoui A
DateDeposition: 2007-08-31, Header release: 2007-09-12, Map release: 2007-09-12, Last update: 2011-05-26
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 380, Made by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 380, Made by UCSF CHIMERA

Supplemental images

1422.gif
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Similar strucutres (beta)

Diagram

EMDB-5592

EMDB-1214
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleMol. Microbiol., Vol. 39, Issue 3, Page 652-63, Year 2001
TitleStructure and composition of the Shigella flexneri "needle complex", a part of its type III secreton.
AuthorsA Blocker, N Jouihri, E Larquet, P Gounon, F Ebel, C Parsot, P Sansonetti, A Allaoui
Unité de Pathogénie Microbienne Moléculaire, INSERM U389, Institut Pasteur, 25-28 rue du Dr Roux, 75724 Paris Cedex 15, France.
KeywordsAdhesins, Bacterial, Amino Acid Sequence, Bacterial Outer Membrane Proteins (chemistry), Bacterial Proteins (chemistry), Image Processing, Computer-Assisted, Lipoproteins (chemistry), Microscopy, Electron, Molecular Sequence Data, Mutation, MxiD protein, Shigella, MxiH protein, Shigella, Protein Transport, Sequence Analysis, DNA, Shigella flexneri (genetics), Virulence, invasin, Yersinia (114073-91-5), mxiJ protein, Shigella flexneri (149059-06-3)
LinksPubMed: 11169106
Map
FileEMD-1422.map ( map file in CCP4 format, 108001 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)X (Row.)Y (Col.)

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density

Histogram

Histogram (log scale)
Contour Level:103, 380 (movie #1):
Minimum - Maximum: -257.841 - 820.019
Average (Standard dev.): -12.8026 (115.599)
Data Typefloat (32-bit)
Space Group Number1
Map Geometry
Axis orderYXZ
Dimensions300300300
Origin-150-150-149
Limit149149150
Spacing300300300
Unit CellA= B= C: 660 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 2.2 A
CCP4 map header info
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
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-257.841820.019-12.803
Annotation DetailsBasal Body of Shigella flexneri T3SS - needle removed
Supplement
Images
Images

1422.gif
Sample
Nameneedle complex or basal body of the Shigella flexneri T3SS
Oligomeric Statenot yet fully determined
Number of Components5
Component #1: protein - MxiH
Scientific nameMxiH
Theoretical Mass9.265 MDa
Experimental Mass9.265 MDa
Detailsnone; copy number is approximative
Oligomeric Detailshelical polymer
Number of Copies120
Scientific Name of SpeciesShigella flexneri
NCBI taxonomy623
StrainM90T
Recombinant expressionNo
Natural SourceOrganelle: T3SS
Cell Location: extracellular
Organ Or Tissue: bacterium
LinksInter Pro: IPR:011841
Component #2: protein - MxiI
Scientific nameMxiI
Theoretical Mass10.633 MDa
Experimental Mass10.633 MDa
Detailsnone; Copy number is approximative
Oligomeric Detailsprobably helical
Number of Copies20
Scientific Name of SpeciesShigella flexneri
NCBI taxonomy623
StrainM90T
Recombinant expressionNo
Natural SourceCell Location: periplasmic
Cell: bacterium
Organelle: T3SS
Component #3: protein - MxiD
Scientific nameMxiD
Theoretical Mass60.749 MDa
Experimental Mass63.218 MDa
Detailsexperimental weight is theoretical weight, with predicted signal sequence removed; oligomeric state currently unknown
Oligomeric Detailsoligomer
Scientific Name of SpeciesShigella flexneri
NCBI taxonomy623
StrainM90T
Recombinant expressionNo
Natural SourceCell Location: outer membrane
Organelle: T3SS
Cell: bacterium
LinksInter Pro: IPR:003522, Gene Ontology: GO:0015448
Component #4: protein - MxiG
Scientific nameMxiG
Theoretical Mass43.002 MDa
Experimental Mass43.002 MDa
Detailsno signal sequence cleavage in this protein; oligomeric state unknown
Oligomeric Detailsoligomer
Scientific Name of SpeciesShigella flexneri
NCBI taxonomy623
StrainM90T
Recombinant expressionNo
Natural SourceOrganelle: T3SS
Cell Location: inner membrane
Cell: bacterium
LinksGene Ontology: GO:0005515
Component #5: protein - MxiJ
Scientific nameMxiJ
Theoretical Mass25.488 MDa
Experimental Mass27.509 MDa
Detailsexperimental weight is theoretical weight, with predicted signal sequence removed; oligomeric state unknown
Oligomeric Detailsoligomer
Scientific Name of SpeciesShigella flexneri
NCBI taxonomy623
StrainM90T
Recombinant expressionNo
Natural SourceCell: bacterium
Organelle: T3SS
Cell Location: inner membrane
LinksGene Ontology: GO:0005515, Inter Pro: IPR:006182
Experiment
Sample Preparation
Staining1% uranyl acetate pH 7.5
Specimen Support Detailscarbon-coated glow-discharged copper grids
Specimen Stateparticle
BufferDetails: 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
Vitrification
Cryogen NameETHANE
Imaging
MicroscopeFEI/PHILIPS CM120T
Detailslow-dose mode used, imaging done in 1999-2000
Electron Gun
Electron SourceLAB6
Accelerating Voltage100 kV
Electron Dose10 e/A**2
Illumination ModeSPOT SCAN
Lens
MagnificationNominal: 45000
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Defocus600 nm - 1200 nm
Specimen Holder
HolderEucentric
ModelOTHER
Temperature293 K ( 293 - 293 K)
Camera
DetectorKodak SO163
Image Acquisition
Number of Digital Images20
Sampling Size10
ScannerOTHER
DetailsHi-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)
Processing
Methodsingle particle reconstruction
3D reconstruction
Algorithmsingle particle
SoftwareSPIDER
Resolution By Author17 A
Resolution MethodFourier ring correlation and differential phase residual
Details1) 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).
Single Particle
Number of Class Averages5
Number of Projections868
DetailsParticles selected using interactive WEB selection program
Download
Data from EMDB
Header (meta data in XML format)emd-1422.xml (12.3 KB)
Map dataemd_1422.map.gz (3.3 MB)
Images1422.gif (17.5 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1422
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 5.4 MB
Session file for UCSF-Chimera, 27.4 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 5 MB
Session file for UCSF-Chimera, 27.5 KB