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- EMDB-5352: Structure of a type III secretion needle -

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Basic information

Entry
Database: EMDB / ID: 5352
TitleStructure of a type III secretion needle
Keywordstype III secretion system / needle / helical filament
SampleShigella needle
SourceShigella flexneri / bacteria / シゲラ・フレクスネリ, フレクスナー赤痢菌
Map dataThis is an reconstruction of the type III secretion needle
Methodhelical reconstruction, at 7.7 A resolution
AuthorsFujii T / Cheung M / Blanco A / Kato T / Blocker AJ / Namba K
CitationProc. Natl. Acad. Sci. U.S.A., 2012, 109, 4461-4466

Proc. Natl. Acad. Sci. U.S.A., 2012, 109, 4461-4466 StrPapers
Structure of a type III secretion needle at 7-Å resolution provides insights into its assembly and signaling mechanisms.
Takashi Fujii / Martin Cheung / Amandine Blanco / Takayuki Kato / Ariel J Blocker / Keiichi Namba

DateDeposition: Nov 2, 2011 / Header (metadata) release: Nov 28, 2011 / Map release: Feb 20, 2012 / Last update: Nov 2, 2011

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 6.76
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 6.76
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-3j0r
  • Surface level: 6.76
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-3j0r
  • Surface level: 6.76
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-2mme
  • Surface level: 6.76
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-2mme
  • Surface level: 6.76
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_5352.map.gz (map file in CCP4 format, 3908 KB)
Projections & slices

Image control

Size
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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.

Voxel sizeX=Y=Z: 1.68 A
Density
Contour Level:6.76 (by author), 6.76 (movie #1):
Minimum - Maximum-11.36894798 - 22.53497505
Average (Standard dev.)0.10644222 (2.6820209)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions100100100
Origin-50-50-50
Limit494949
Spacing100100100
CellA=B=C: 168 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

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
D min/max/mean-11.36922.5350.106

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Supplemental data

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Sample components

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Entire Shigella needle

EntireName: Shigella needle / Number of components: 1 / Oligomeric State: helical assembly of MxiH

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Component #1: protein, MxiH

ProteinName: MxiH / a.k.a: MxiH / Recombinant expression: Yes
SourceSpecies: Shigella flexneri / bacteria / シゲラ・フレクスネリ, フレクスナー赤痢菌

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Experimental details

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Sample preparation

Specimen statefilament
Helical parametersHand: RIGHT HANDED / Delta z: 4.3 A / Delta phi: 64.06 deg.
Sample solutionBuffer solution: 20 mM Tris, pH 7.4, 150 mM NaCl, 2mM MgSO4 / pH: 7.4
VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Humidity: 100 % / Method: Blot for 3.5 seconds before plunging / Details: Vitrification instrument: Vitrobot

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Electron microscopy imaging

ImagingMicroscope: JEOL 3200FSC / Date: Jul 2, 2008
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 20 e/A2 / Illumination mode: FLOOD BEAM
LensMagnification: 50000 X (nominal), 89285 X (calibrated) / Cs: 1.6 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 2000 nm / Energy filter: JEOL Omega filter / Energy window: 0-10 eV
Specimen HolderHolder: top entry / Model: OTHER / Temperature: 50 K ( 50 - 60 K)
CameraDetector: TVIPS TEMCAM-F415 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 330 / Sampling size: 15 microns / Bit depth: 16

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Image processing

ProcessingMethod: helical reconstruction
3D reconstructionAlgorithm: Projection Matching / Software: SPIDER / CTF correction: CTFFIND3 Each particle / Resolution: 7.7 A / Resolution method: FSC 0.5

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Atomic model buiding

Output model

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