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Structure of a type III secretion needle

by helical reconstruction, at 7.7 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 6.76, Image by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 6.76, Image by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-3j0r, Surface level: 6.76, Image by UCSF CHIMERA

#4: Surface view with fitted model, atomic models: PDB-3j0r, Surface level: 6.76, Image by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 5352
TitleStructure of a type III secretion needle
MapThis is an reconstruction of the type III secretion needle
SampleShigella needle
Keywordstype III secretion system, needle, helical filament
AuthorsFujii T, Cheung M, Blanco A, Kato T, Blocker AJ, Namba K
DateDeposition: 2011-11-02, Header release: 2011-11-28, Map release: 2012-02-20, Last update: 2012-03-06
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 6.76, Image by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 6.76, Image by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-3j0r, Surface level: 6.76, Image by UCSF CHIMERA

#4: Surface view with fitted model, atomic models: PDB-3j0r, Surface level: 6.76, Image by UCSF CHIMERA

Supplemental images
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries

PDB-3j0r

CiteFit

Cite: data citing same article

Fit: output model of fitting

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Article
Citation - Primary
ArticleProc. Natl. Acad. Sci. U.S.A., Vol. 109, Issue 12, Page 4461-6, Year 2012
TitleStructure of a type III secretion needle at 7-Å resolution provides insights into its assembly and signaling mechanisms.
AuthorsTakashi Fujii, Martin Cheung, Amandine Blanco, Takayuki Kato, Ariel J Blocker, Keiichi Namba
Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan.
KeywordsBacterial Proteins (chemistry), Calibration, Cell Membrane (metabolism), Cryoelectron Microscopy (methods), Image Processing, Computer-Assisted, Models, Molecular, Molecular Conformation, MxiH protein, Shigella, Polymers (chemistry), Protein Conformation, Protein Structure, Secondary, Protein Structure, Tertiary, Shigella flexneri (metabolism), Signal Transduction, Temperature
LinksDOI: 10.1073/pnas.1116126109, PubMed: 22388746, PMC: PMC3311390
Map
Fileemd_5352.map.gz ( map file in CCP4 format, 3908 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
100 pix
1.68 A/pix
= 168. A
100 pix
1.68 A/pix
= 168. A
100 pix
1.68 A/pix
= 168. A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:6.76 (by author), 6.76 (movie #1):
Minimum - Maximum: -11.36894798 - 22.53497505
Average (Standard dev.): 0.10644222 (2.6820209)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions100100100
Origin-50-50-50
Limit494949
Spacing100100100
Unit CellA= B= C: 168 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 1.68 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z1.681.681.68
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z168.000168.000168.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS-50-50-50
NC/NR/NS100100100
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-11.36922.5350.106
Annotation DetailsThis is an reconstruction of the type III secretion needle
Supplement
Images
Images
Sample
NameShigella needle
Number of Components1
Oligomeric Statehelical assembly of MxiH
Component #1: protein - MxiH
Scientific nameMxiH
Scientific Name of SpeciesShigella flexneri
NCBI taxonomy623
Recombinant expressionYes
Experiment
Sample Preparation
Helical ParametersDelta Z: 4.3 A
Delta Phi: 64.06 degrees
Hand: RIGHT HANDED
Specimen Statefilament
BufferpH: 7.4
Details: 20 mM Tris, pH 7.4, 150 mM NaCl, 2mM MgSO4
Vitrification
MethodBlot for 3.5 seconds before plunging
Cryogen NameETHANE
DetailsVitrification instrument: Vitrobot
Humidity100
InstrumentFEI VITROBOT
Imaging
MicroscopeJEOL 3200FSC
Date02-JUL-2008
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Electron Dose20 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 50000, Calibrated: 89285
Nominal Cs1.6 mm
Imaging ModeBRIGHT FIELD
Defocus1000 nm - 2000 nm
Energy FilterEnergy Filter: JEOL Omega filter , Energy Window: 0-10 eV
Specimen Holder
Holdertop entry
ModelOTHER
Temperature50 K ( 50 - 60 K)
Camera
DetectorTVIPS TEMCAM-F415 (4k x 4k)
Image Acquisition
Number of Digital Images330
Sampling Size15
Quant Bit Number16
Processing
Methodhelical reconstruction
3D reconstruction
AlgorithmProjection Matching
SoftwareSPIDER
CTF CorrectionCTFFIND3 Each particle
Resolution By Author7.7 A
Resolution MethodFSC 0.5
Atomic Model Fitting
Fitted Coordinate
PDB entry ID
Download
Data from EMDB
Header (meta data in XML format)emd-5352.xml (6.9 KB)
Map dataemd_5352.map.gz (3.6 MB)
Imagesemd_5352_1.jpg (61.4 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-5352
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 4.8 MB
Session file for UCSF-Chimera, 26.5 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.1 MB
.webm (WebM/VP8 format), 4.5 MB
Session file for UCSF-Chimera, 26.5 KB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
.webm (WebM/VP8 format), 5.1 MB
Session file for UCSF-Chimera, 1.1 MB
movie #4
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 4.6 MB
Session file for UCSF-Chimera, 173.1 KB