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- EMDB-8611: Negative stain reconstruction of E. coli MCE protein YebT -

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Basic information

Entry
Database: EMDB / ID: 8611
TitleNegative stain reconstruction of E. coli MCE protein YebT
SampleYebT
SourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Map dataE. coli MCE protein PqiB, periplasmic domain
Methodsingle particle reconstruction, at 25 Å resolution
AuthorsBhabha G / Ekiert DC
CitationCell, 2017, 169, 273-285.e17

Cell, 2017, 169, 273-285.e17 StrPapers
Architectures of Lipid Transport Systems for the Bacterial Outer Membrane.
Damian C Ekiert / Gira Bhabha / Georgia L Isom / Garrett Greenan / Sergey Ovchinnikov / Ian R Henderson / Jeffery S Cox / Ronald D Vale

DateDeposition: Feb 21, 2017 / Header (metadata) release: Apr 12, 2017 / Map release: Apr 12, 2017 / Last update: Feb 21, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.086
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.086
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


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Supplemental images

Downloads & links

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Map

Fileemd_8611.map.gz (map file in CCP4 format, 3539 KB)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
96 pix
4.42 Å/pix.
= 424.32 Å
96 pix
4.42 Å/pix.
= 424.32 Å
96 pix
4.42 Å/pix.
= 424.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 4.42 Å
Density
Contour Level:0.086 (by author), 0.086 (movie #1):
Minimum - Maximum-0.13925247 - 0.23584455
Average (Standard dev.)0.0008635771 (0.016180625)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions969696
Origin000
Limit959595
Spacing969696
CellA=B=C: 424.32 Å
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z4.424.424.42
M x/y/z969696
origin x/y/z0.0000.0000.000
length x/y/z424.320424.320424.320
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS969696
D min/max/mean-0.1390.2360.001

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Supplemental data

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Sample components

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Entire YebT

EntireName: YebT / Number of components: 2

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Component #1: protein, YebT

ProteinName: YebT / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #2: protein, YebT

ProteinName: YebT / Recombinant expression: No
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionpH: 8
VitrificationCryogen name: NONE

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI 12
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Electron dose: 10 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN ULTRASCAN 4000 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 4787
3D reconstructionSoftware: relion / Resolution: 25 Å / Resolution method: FSC 0.143 CUT-OFF

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