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- EMDB-8612: Negative stain reconstruction of E. coli MCE protein PqiB -

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Basic information

Entry
Database: EMDB / ID: 8612
TitleNegative stain reconstruction of E. coli MCE protein PqiB
Map dataE. coli MCE protein PqiB, periplasmic domain
SampleYebT:
PqiB
Function / homologyMce/MlaD / MlaD protein / outer membrane-bounded periplasmic space / integral component of membrane / plasma membrane / Paraquat-inducible protein B
Function and homology information
SourceEscherichia coli (E. coli)
Methodsingle particle reconstruction / 25 Å resolution
AuthorsBhabha G / Ekiert DC
CitationJournal: Cell / Year: 2017
Title: Architectures of Lipid Transport Systems for the Bacterial Outer Membrane.
Authors: Damian C Ekiert / Gira Bhabha / Georgia L Isom / Garrett Greenan / Sergey Ovchinnikov / Ian R Henderson / Jeffery S Cox / Ronald D Vale
Abstract: How phospholipids are trafficked between the bacterial inner and outer membranes through the hydrophilic space of the periplasm is not known. We report that members of the mammalian cell entry (MCE) ...How phospholipids are trafficked between the bacterial inner and outer membranes through the hydrophilic space of the periplasm is not known. We report that members of the mammalian cell entry (MCE) protein family form hexameric assemblies with a central channel capable of mediating lipid transport. The E. coli MCE protein, MlaD, forms a ring associated with an ABC transporter complex in the inner membrane. A soluble lipid-binding protein, MlaC, ferries lipids between MlaD and an outer membrane protein complex. In contrast, EM structures of two other E. coli MCE proteins show that YebT forms an elongated tube consisting of seven stacked MCE rings, and PqiB adopts a syringe-like architecture. Both YebT and PqiB create channels of sufficient length to span the periplasmic space. This work reveals diverse architectures of highly conserved protein-based channels implicated in the transport of lipids between the membranes of bacteria and some eukaryotic organelles.
DateDeposition: Feb 21, 2017 / Header (metadata) release: Apr 12, 2017 / Map release: Apr 12, 2017 / Last update: Feb 14, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.048
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.048
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_8612.map.gz (map file in CCP4 format, 1049 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
64 pix
4.42 Å/pix.
= 282.88 Å
64 pix
4.42 Å/pix.
= 282.88 Å
64 pix
4.42 Å/pix.
= 282.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.42 Å
Density
Contour Level:0.048 (by author), 0.048 (movie #1):
Minimum - Maximum-0.16012093 - 0.30318454
Average (Standard dev.)-0.00016570522 (0.024086941)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions646464
Origin000
Limit636363
Spacing646464
CellA=B=C: 282.88 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.424.424.42
M x/y/z646464
origin x/y/z0.0000.0000.000
length x/y/z282.880282.880282.880
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ281156
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS646464
D min/max/mean-0.1600.303-0.000

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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 (E. coli)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #2: protein, PqiB

ProteinName: PqiB / Recombinant expression: No
Source (engineered)Expression System: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle
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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