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- EMDB-8610: Structure of E. coli MCE protein PqiB, periplasmic domain -

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Basic information

Entry
Database: EMDB / ID: EMD-8610
TitleStructure of E. coli MCE protein PqiB, periplasmic domain
Map dataE. coli MCE protein PqiB, periplasmic domain
Sample
  • Complex: MlaFEDB
    • Protein or peptide: MlaF
    • Protein or peptide: MlaE
    • Protein or peptide: MlaD
    • Protein or peptide: MlaB
Function / homology: / Mce/MlaD / MlaD protein / intermembrane lipid transfer / membrane organization / outer membrane-bounded periplasmic space / identical protein binding / plasma membrane / Intermembrane transport protein PqiB
Function and homology information
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 10.0 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 20, 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: 0.139
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.139
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8610.png

Downloads & links

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Map

FileDownload / File: emd_8610.map.gz / Format: CCP4 / Size: 1.2 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.)
3.03 Å/pix.
x 68 pix.
= 206.04 Å		3.03 Å/pix.
x 68 pix.
= 206.04 Å		3.03 Å/pix.
x 68 pix.
= 206.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.03 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.139 / Movie #1: 0.139
Minimum - Maximum-0.35875395 - 0.62261736
Average (Standard dev.)0.007208153 (±0.041473098)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions686868
Spacing686868
CellA=B=C: 206.04 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.033.033.03
M x/y/z686868
origin x/y/z0.0000.0000.000
length x/y/z206.040206.040206.040
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/NS686868
D min/max/mean-0.3590.6230.007

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Supplemental data

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Sample components

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Entire : MlaFEDB

EntireName: MlaFEDB
Components
  • Complex: MlaFEDB
    • Protein or peptide: MlaF
    • Protein or peptide: MlaE
    • Protein or peptide: MlaD
    • Protein or peptide: MlaB

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Supramolecule #1: MlaFEDB

SupramoleculeName: MlaFEDB / 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: MlaF

MacromoleculeName: MlaF / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MEQSVANLVD MRDVSFTRGN RCIFDNISL TVPRGKITAI M GPSGIGKT TLLRLIGGQI AP DHGEILF DGENIPAMSR SRL YTVRKR MSMLFQSGAL FTDM NVFDN VAYPLREHTQ LPAPL LHST VMMKLEAVGL RGAAKL MPS ELSGGMARRA ALARAIA LE ...String:
MEQSVANLVD MRDVSFTRGN RCIFDNISL TVPRGKITAI M GPSGIGKT TLLRLIGGQI AP DHGEILF DGENIPAMSR SRL YTVRKR MSMLFQSGAL FTDM NVFDN VAYPLREHTQ LPAPL LHST VMMKLEAVGL RGAAKL MPS ELSGGMARRA ALARAIA LE PDLIMFDEPF VGQDPITM G VLVKLISELN SALGVTCVV VSHDVPEVLS IADHAWILAD KKIVAHGSA QALQANPDPR V RQFLDGIA DGPVPFRYPA GD YHADLLP GS

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Macromolecule #2: MlaE

MacromoleculeName: MlaE / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
SequenceString: MLLNALASLG HKGIKTLRTF GRAGLMLFN ALVGKPEFRK H APLLVRQL YNVGVLSMLI IV VSGVFIG MVLGLQGYLV LTT YSAETS LGMLVALSLL RELG PVVAA LLFAGRAGSA LTAEI GLMR ATEQLSSMEM MAVDPL RRV ISPRFWAGVI SLPLLTV IF ...String:
MLLNALASLG HKGIKTLRTF GRAGLMLFN ALVGKPEFRK H APLLVRQL YNVGVLSMLI IV VSGVFIG MVLGLQGYLV LTT YSAETS LGMLVALSLL RELG PVVAA LLFAGRAGSA LTAEI GLMR ATEQLSSMEM MAVDPL RRV ISPRFWAGVI SLPLLTV IF VAVGIWGGSL VGVSWKGI D SGFFWSAMQN AVDWRMDLV NCLIKSVVFA ITVTWISLFN GYDAIPTSA GISRATTRTV V HSSLAVLG LDFVLTALMF GN

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Macromolecule #3: MlaD

MacromoleculeName: MlaD / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
SequenceString: MHHHHHHQHQ HENLYFQGMQ TKKNEIWVG IFLLAALLAA L FVCLKAAN VTSIRTEPTY TL YATFDNI GGLKARSPVS IGG VVVGRV ADITLDPKTY LPRV TLEIE QRYNHIPDTS SLSIR TSGL LGEQYLALNV GFEDPE LGT AILKDGDTIQ DTKSAMV LE ...String:
MHHHHHHQHQ HENLYFQGMQ TKKNEIWVG IFLLAALLAA L FVCLKAAN VTSIRTEPTY TL YATFDNI GGLKARSPVS IGG VVVGRV ADITLDPKTY LPRV TLEIE QRYNHIPDTS SLSIR TSGL LGEQYLALNV GFEDPE LGT AILKDGDTIQ DTKSAMV LE DLIGQFLYGS KGDDNKNS G DAPAAAPGNN ETTEPVGTT K

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Macromolecule #4: MlaB

MacromoleculeName: MlaB / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
SequenceString:
MSESLSWMQT GDTLALSGEL DQDVLLPLW EMREEAVKGI T CIDLSRVS RVDTGGLALL LH LIDLAKK QGNNVTLQGV NDK VYTLAK LYNLPADVLP R

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
Details: 20 mM Tris pH 8.0 and 150 mM NaCl, and exchanged from DDM into amphipol A8-35 as described in the manuscript
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 80.0 e/Å2 / Details: 80 e/A2 is total dose for 50 frames
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND4
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 10.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 28012
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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Atomic model buiding 1

Detailscrystal structure of MlaD and homology models for MlaF, MlaE and MlaB were fit into the density as described in the manuscript
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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