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- EMDB-5033: Structure of a type IV secretion system core complex -

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Basic information

Entry
Database: EMDB / ID: EMD-5033
TitleStructure of a type IV secretion system core complex
Map datavolume
Sample
  • Sample: traN/traO/traF complex encoded by pKM101 Digested with 0.002 mg ml-1 of trypsin for 30 min at 4 degrees Celsius.
  • Protein or peptide: traF
  • Protein or peptide: traO
  • Protein or peptide: traN
Keywordsbacterial secretion / type IV secretion / vir / tra
Methodsingle particle reconstruction / negative staining / Resolution: 19.0 Å
AuthorsFronzes R / Schafer E / Wang L / Saibil H / Orlova E / Waksman G
CitationJournal: Science / Year: 2009
Title: Structure of a type IV secretion system core complex.
Authors: Rémi Fronzes / Eva Schäfer / Luchun Wang / Helen R Saibil / Elena V Orlova / Gabriel Waksman /
Abstract: Type IV secretion systems (T4SSs) are important virulence factors used by Gram-negative bacterial pathogens to inject effectors into host cells or to spread plasmids harboring antibiotic resistance ...Type IV secretion systems (T4SSs) are important virulence factors used by Gram-negative bacterial pathogens to inject effectors into host cells or to spread plasmids harboring antibiotic resistance genes. We report the 15 angstrom resolution cryo-electron microscopy structure of the core complex of a T4SS. The core complex is composed of three proteins, each present in 14 copies and forming a approximately 1.1-megadalton two-chambered, double membrane-spanning channel. The structure is double-walled, with each component apparently spanning a large part of the channel. The complex is open on the cytoplasmic side and constricted on the extracellular side. Overall, the T4SS core complex structure is different in both architecture and composition from the other known double membrane-spanning secretion system that has been structurally characterized.
History
DepositionNov 10, 2008-
Header (metadata) releaseNov 18, 2008-
Map releaseApr 15, 2009-
UpdateApr 15, 2009-
Current statusApr 15, 2009Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.021
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.021
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5033_1.png

Downloads & links

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Map

FileDownload / File: emd_5033.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationvolume
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.5 Å/pix.
x 200 pix.
= 500. Å		2.5 Å/pix.
x 200 pix.
= 500. Å		2.5 Å/pix.
x 200 pix.
= 500. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.5 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.0211 / Movie #1: 0.021
Minimum - Maximum-0.262118 - 0.332674
Average (Standard dev.)0.000130292 (±0.0114328)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 500 Å
α=β=γ: 90 °

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-0.2620.3330.000

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Supplemental data

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Sample components

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Entire : traN/traO/traF complex encoded by pKM101 Digested with 0.002 mg m...

EntireName: traN/traO/traF complex encoded by pKM101 Digested with 0.002 mg ml-1 of trypsin for 30 min at 4 degrees Celsius.
Components
  • Sample: traN/traO/traF complex encoded by pKM101 Digested with 0.002 mg ml-1 of trypsin for 30 min at 4 degrees Celsius.
  • Protein or peptide: traF
  • Protein or peptide: traO
  • Protein or peptide: traN

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Supramolecule #1000: traN/traO/traF complex encoded by pKM101 Digested with 0.002 mg m...

SupramoleculeName: traN/traO/traF complex encoded by pKM101 Digested with 0.002 mg ml-1 of trypsin for 30 min at 4 degrees Celsius.
type: sample / ID: 1000 / Details: monodisperse / Oligomeric state: 14-mer / Number unique components: 3
Molecular weightExperimental: 868 KDa / Theoretical: 700 KDa / Method: gel filtration

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Macromolecule #1: traF

MacromoleculeName: traF / type: protein_or_peptide / ID: 1 / Name.synonym: traF / Number of copies: 14 / Oligomeric state: 14-mer / Recombinant expression: Yes
Source (natural)Strain: BL21 / Cell: Escherichia coli / Location in cell: inner membrane
Molecular weightTheoretical: 40 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pASK-IBA3c

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Macromolecule #2: traO

MacromoleculeName: traO / type: protein_or_peptide / ID: 2 / Name.synonym: traO / Number of copies: 14 / Oligomeric state: 14-mer / Recombinant expression: Yes
Source (natural)Strain: BL21 / Cell: Escherichia coli / Location in cell: outer membrane
Molecular weightTheoretical: 30 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pASK-IBA3c

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Macromolecule #3: traN

MacromoleculeName: traN / type: protein_or_peptide / ID: 3 / Name.synonym: traN / Number of copies: 14 / Oligomeric state: 14-mer / Recombinant expression: Yes
Source (natural)Strain: BL21 / Cell: Escherichia coli / Location in cell: outer membrane
Molecular weightTheoretical: 5 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pASK-IBA3c

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.5 mg/mL
BufferDetails: 50 mM Tris-HCL, 200 mM NaCl, 10 mM LDAO
StainingType: NEGATIVE / Details: 2% uranyl acetate
GridDetails: carbon coated copper grids
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI 12
TemperatureMin: 293 K / Max: 293 K / Average: 293 K
DateJan 1, 2008
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 22 / Average electron dose: 20 e/Å2 / Od range: 2 / Bits/pixel: 8
Electron beamAcceleration voltage: 120 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsCalibrated magnification: 42000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 42000
Sample stageSpecimen holder: side entry room temperature / Specimen holder model: OTHER

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Image processing

Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 19.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: imagic / Details: final maps were calculated from 2201 particles / Number images used: 2201
Final two d classificationNumber classes: 150

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