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- EMDB-3877: Inner membrane Bcs complex (E. coli) -

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Basic information

Entry
Database: EMDB / ID: 3877
TitleInner membrane Bcs complex (E. coli)
Map dataAn inner membrane subcomplex of the E. coli cellulose secretion system (Bcs). The complex was purified from solubilised membranes of Bl21(DE3) cells over-expressing the BcsRQAB subunits.
SampleBcs inner membrane sub-complex.:
SourceEscherichia coli (E. coli)
Methodsingle particle reconstruction / negative staining / 21.1 Å resolution
AuthorsKrasteva PV / Fronzes R
CitationJournal: Nat Commun / Year: 2017
Title: Insights into the structure and assembly of a bacterial cellulose secretion system.
Authors: Petya Violinova Krasteva / Joaquin Bernal-Bayard / Laetitia Travier / Fernando Ariel Martin / Pierre-Alexandre Kaminski / Gouzel Karimova / Rémi Fronzes / Jean-Marc Ghigo
DateDeposition: Sep 14, 2017 / Header (metadata) release: Dec 20, 2017 / Map release: Dec 27, 2017 / Last update: Dec 27, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_3877.map.gz (map file in CCP4 format, 23329 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
180 pix
1.9 Å/pix.
= 342. Å
180 pix
1.9 Å/pix.
= 342. Å
180 pix
1.9 Å/pix.
= 342. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.9 Å
Density
Contour Level:0.015 (by author), 0.015 (movie #1):
Minimum - Maximum-0.09078771 - 0.12465287
Average (Standard dev.)0.00024227778 (0.0091167325)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions180180180
Origin000
Limit179179179
Spacing180180180
CellA=B=C: 342 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.91.91.9
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z342.000342.000342.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS180180180
D min/max/mean-0.0910.1250.000

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Supplemental data

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Sample components

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Entire Bcs inner membrane sub-complex.

EntireName: Bcs inner membrane sub-complex.
Details: Sample purified using BcsA as bait from solubilised E. coli Bl21(DE3) cells over-expressing the BcsRQAB sub-units of cellulose-secreting E. coli 1094.
Number of components: 1
MassTheoretical: 1000 kDa

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Component #1: protein, Bcs inner membrane sub-complex.

ProteinName: Bcs inner membrane sub-complex.
Details: Sample purified using BcsA as bait from solubilised E. coli Bl21(DE3) cells over-expressing the BcsRQAB sub-units of cellulose-secreting E. coli 1094.
Recombinant expression: No
MassTheoretical: 1000 kDa
SourceSpecies: Escherichia coli (E. coli) / Strain: 1094
Source (engineered)Expression System: Escherichia coli (E. coli) / Vector: pCDF-Duet / Strain: Bl21(DE3)
Source (natural)Location in cell: inner membrane

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: negative staining
Sample solutionSpecimen conc.: 0.1 mg/ml
Buffer solution: 20 mM HEPES 8.0 120 mM NaCl 10 glycerol 5 mM MgCl2 10 uM AppCp 2 uM c-di-GMP 0.008% LM-NPG cOmplete protease inhibitors
pH: 8
Staining5 ul of sample were spotted on glow-discharged carbon-coated copper grids and incubated for 1 minute. Liquid was blotted off and the sample was passed through 3 drops of 10 ul 2% uranyl acetate with a 30-second incubation over the third. After that the stain was blotted off and the grid was air-dried.
VitrificationCryogen name: NONE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 12 e/Å2 / Illumination mode: OTHER
LensMagnification: 50000 X (nominal) / Imaging mode: BRIGHT FIELD / Defocus: - 500 nm
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 14362
3D reconstructionSoftware: RELION
CTF correction: CTF correction was carried out in EMAN2.0 (e2ctf) in two rounds, before and after structure factor generation
Resolution: 21.1 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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