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- EMDB-5035: Structure of a type IV secretion system core complex -

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Basic information

Entry
Database: EMDB / ID: 5035
TitleStructure of a type IV secretion system core complex
Keywordsbacterial secretion / type IV secretion / vir / tra
SampletraN/traO/traF encoded by pKM101. traN is mutated to replace cys15 by ser (lipidation site)
Map datavolume
Methodsingle particle reconstruction, at 18 Å resolution
AuthorsFronzes R / Schafer E / Wang L / Saibil H / Orlova E / Waksman G
CitationScience, 2009, 323, 266-268

Science, 2009, 323, 266-268 StrPapers
Structure of a type IV secretion system core complex.
Rémi Fronzes / Eva Schäfer / Luchun Wang / Helen R Saibil / Elena V Orlova / Gabriel Waksman

DateDeposition: Nov 10, 2008 / Header (metadata) release: Nov 18, 2008 / Map release: Apr 15, 2009 / Last update: Apr 15, 2009

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.025
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_5035.map.gz (map file in CCP4 format, 31251 KB)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
200 pix
2.5 Å/pix.
= 500. Å
200 pix
2.5 Å/pix.
= 500. Å
200 pix
2.5 Å/pix.
= 500. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.5 Å
Density
Contour Level:0.025, 0.025 (movie #1):
Minimum - Maximum-0.384705 - 0.385275
Average (Standard dev.)0.000218033 (0.0162388)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions200200200
Origin000
Limit199199199
Spacing200200200
CellA=B=C: 500 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.52.52.5
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z500.000500.000500.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-127-127-127
NX/NY/NZ255255255
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.3850.3850.000

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Supplemental data

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Sample components

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Entire traN/traO/traF encoded by pKM101. traN is mutated to replace cys1...

EntireName: traN/traO/traF encoded by pKM101. traN is mutated to replace cys15 by ser (lipidation site)
Details: aggregates a high concentration / Number of components: 3 / Oligomeric State: 14
MassTheoretical: 1.05 MDa / Experimental: 1.1 MDa / Measured by: gel filtration

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Component #1: protein, traF

ProteinName: traF / a.k.a: traF / Oligomeric Details: 14-mer / Number of Copies: 14 / Recombinant expression: Yes
MassTheoretical: 40 kDa
SourceStrain: BL21
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Vector: pASK-IBA3c
Source (natural)Location in cell: inner membrane / Cell: Escherichia coli

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Component #2: protein, traO

ProteinName: traO / a.k.a: traO / Oligomeric Details: 14-mer / Recombinant expression: Yes / Number of Copies: 14
MassTheoretical: 30 kDa
SourceStrain: BL21
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Vector: pASK-IBA3c
Source (natural)Location in cell: outer membrane / Cell: Escherichia coli

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Component #3: protein, traO

ProteinName: traO / a.k.a: traO / Oligomeric Details: 14-mer / Details: non lipidated subunit / Number of Copies: 14 / Recombinant expression: Yes
MassTheoretical: 5 kDa
SourceStrain: BL21
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Vector: pASK-IBA3c
Source (natural)Location in cell: outer membrane / Cell: Escherichia coli

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.5 mg/ml / Buffer solution: 50 mM Tris-HCL, 200 mM NaCl, 10 mM LDAO
Support filmcarbon coated copper grids
Staining2% uranyl acetate
VitrificationInstrument: NONE / Cryogen name: NONE

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI 12 / Date: Jan 1, 2008
Electron gunElectron source: TUNGSTEN HAIRPIN / Accelerating voltage: 120 kV / Electron dose: 20 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 42000 X (nominal), 42000 X (calibrated) / Cs: 2.2 mm / Imaging mode: BRIGHT FIELD / Defocus: 800 - 2000 nm
Specimen HolderHolder: side entry room temperature / Model: OTHER / Temperature: 293 K ( 293 - 293 K)
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 15 / Scanner: ZEISS SCAI / Sampling size: 7 microns / Bit depth: 8 / OD range: 2

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Image processing

ProcessingMethod: single particle reconstruction / Number of class averages: 300 / Number of projections: 1231 / Applied symmetry: C14 (14 fold cyclic)
3D reconstructionAlgorithm: common lines / Software: imagic / Details: final map was calculated from 300 class averages / Resolution: 18 Å / Resolution method: FSC 0.5

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