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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: EMD-8611
TitleNegative stain reconstruction of E. coli MCE protein YebT
Map dataE. coli MCE protein PqiB, periplasmic domain
Sample
  • Complex: YebT
    • Protein or peptide: YebT
Function / homology: / Mce/MlaD / MlaD protein / intermembrane lipid transfer / membrane organization / outer membrane-bounded periplasmic space / identical protein binding / plasma membrane / Lipophilic envelope-spanning tunnel protein B
Function and homology information
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / negative staining / Resolution: 25.0 Å
AuthorsBhabha G / Ekiert DC
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)K99GM112982 United States
Howard Hughes Medical Institute (HHMI) United States
Damon Runyon Cancer Research FoundationDRG-2140-12 United States
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.
History
DepositionFeb 21, 2017-
Header (metadata) releaseApr 12, 2017-
Map releaseApr 12, 2017-
UpdateDec 11, 2019-
Current statusDec 11, 2019Processing site: RCSB / Status: Released

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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
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8611.png

Downloads & links

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Map

FileDownload / File: emd_8611.map.gz / Format: CCP4 / Size: 3.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationE. coli MCE protein PqiB, periplasmic domain
Projections & slices

Image control

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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.086 / Movie #1: 0.086
Minimum - Maximum-0.13925247 - 0.23584455
Average (Standard dev.)0.0008635771 (±0.016180625)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions969696
Spacing969696
CellA=B=C: 424.32 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/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
α/β/γ90.00090.00090.000
start NX/NY/NZ-51-35-11
NX/NY/NZ11110799
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
Components
  • Complex: YebT
    • Protein or peptide: YebT

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Supramolecule #1: YebT

SupramoleculeName: YebT / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: YebT

MacromoleculeName: YebT / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHMSQETPAS TTEAQIKNKR RISPFWLLP FIALMIASWL I WDSYQDRG NTVTIDFMSA DG IVPGRTP VRYQGVEVGT VQD ISLSDD LRKIEVKVSI KSDM KDALR EETQFWLVTP KASLA GVSG LDALVGGNYI GMMPGK GKE QDHFVALDTQ PKYRLDN GD ...String:
MHMSQETPAS TTEAQIKNKR RISPFWLLP FIALMIASWL I WDSYQDRG NTVTIDFMSA DG IVPGRTP VRYQGVEVGT VQD ISLSDD LRKIEVKVSI KSDM KDALR EETQFWLVTP KASLA GVSG LDALVGGNYI GMMPGK GKE QDHFVALDTQ PKYRLDN GD LMIHLQAPDL GSLNSGSL V YFRKIPVGKV YDYAINPNK QGVVIDVLIE RRFTDLVKKG SRFWNVSGV DANVSISGAK V KLESLAAL VNGAIAFDSP EE SKPAEAE DTFGLYEDLA HSQ RGVIIK LELPSGAGLT ADST PLMYQ GLEVGQLTKL DLNPG GKVT GEMTVDPSVV TLLREN TRI ELRNPKLSLS DANLSAL LT GKTFELVPGD GEPRKEFV V VPGEKALLHE PDVLTLTLT APESYGIDAG QPLILHGVQV GQVIDRKLT SKGVTFTVAI E PQHRELVK GDSKFVVNSR VD VKVGLDG VEFLGASASE WIN GGIRIL PGDKGEMKAS YPLY ANLEK ALENSLSDLP TTTVS LSAE TLPDVQAGSV VLYRKF EVG EVITVRPRAN AFDIDLH IK PEYRNLLTSN SVFWAEGG A KVQLNGSGLT VQASPLSRA LKGAISFDNL SGASASQRKG DKRILYASE TAARAVGGQI T LHAFDAGK LAVGMPIRYL GI DIGQIQT LDLITARNEV QAK AVLYPE YVQTFARGGT RFSV VTPQI SAAGVEHLDT ILQPY INVE PGRGNPRRDF ELQEAT ITD SRYLDGLSII VEAPEAG SL GIGTPVLFRG LEVGTVTG M TLGTLSDRVM IAMRISKRY QHLVRNNSVF WLASGYSLDF GLTGGVVKT GTFNQFIRGG I AFATPPGT PLAPKAQEGK HF LLQESEP KEWREWGTAL PKH QHQHHH HHH

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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

BufferpH: 8
StainingType: NEGATIVE / Material: Uranyl Formate

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Electron microscopy

MicroscopeFEI TECNAI 12
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 10.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 4787
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: RELION (ver. 1.4)
Final angle assignmentType: OTHER / Software - Name: RELION (ver. 1.4)
Final 3D classificationSoftware - Name: RELION (ver. 1.4)

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