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- EMDB-8608: Structure of E. coli MCE protein PqiB, periplasmic domain -

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Basic information

Entry
Database: EMDB / ID: EMD-8608
TitleStructure of E. coli MCE protein PqiB, periplasmic domain
Map dataE. coli MCE protein PqiB, periplasmic domain
Sample
  • Complex: homo hexamer of PqiB
    • Protein or peptide: Paraquat-inducible protein B
KeywordsMCE protein / bacterial lipid transport / TRANSPORT PROTEIN
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: 3.96 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
Damon Runyon Cancer Research FoundationDRG-2140-12 United States
Howard Hughes Medical Institute (HHMI) 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-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.055
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.055
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5uvn
  • Surface level: 0.055
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8608.png

Downloads & links

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Map

FileDownload / File: emd_8608.map.gz / Format: CCP4 / Size: 30.5 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.)
1.31 Å/pix.
x 200 pix.
= 262. Å		1.31 Å/pix.
x 200 pix.
= 262. Å		1.31 Å/pix.
x 200 pix.
= 262. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.31 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.055 / Movie #1: 0.055
Minimum - Maximum-0.18554376 - 0.40328574
Average (Standard dev.)0.0008848738 (±0.010312201)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 262.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.311.311.31
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z262.000262.000262.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.1860.4030.001

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Supplemental data

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Additional map: Additional map, E. coli MCE protein PqiB, periplasmic domain

Fileemd_8608_additional.map
AnnotationAdditional map, E. coli MCE protein PqiB, periplasmic domain
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : homo hexamer of PqiB

EntireName: homo hexamer of PqiB
Components
  • Complex: homo hexamer of PqiB
    • Protein or peptide: Paraquat-inducible protein B

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Supramolecule #1: homo hexamer of PqiB

SupramoleculeName: homo hexamer of PqiB / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli) / Strain: K12
Molecular weightTheoretical: 347 KDa

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Macromolecule #1: Paraquat-inducible protein B

MacromoleculeName: Paraquat-inducible protein B / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: K12
Molecular weightTheoretical: 48.857043 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHHHHHHENL YFQSHQGPEV TLITANAEGI EGGKTTIKSR SVDVGVVESA TLADDLTHVE IKARLNSGME KLLHKDTVFW VVKPQIGRE GISGLGTLLS GVYIELQPGA KGSKMDKYDL LDSPPLAPPD AKGIRVILDS KKAGQLSPGD PVLFRGYRVG S VETSTFDT ...String:
MHHHHHHENL YFQSHQGPEV TLITANAEGI EGGKTTIKSR SVDVGVVESA TLADDLTHVE IKARLNSGME KLLHKDTVFW VVKPQIGRE GISGLGTLLS GVYIELQPGA KGSKMDKYDL LDSPPLAPPD AKGIRVILDS KKAGQLSPGD PVLFRGYRVG S VETSTFDT QKRNISYQLF INAPYDRLVT NNVRFWKDSG IAVDLTSAGM RVEMGSLTTL LSGGVSFDVP EGLDLGQPVA PK TAFVLYD DQKSIQDSLY TDHIDYLMFF KDSVRGLQPG APVEFRGIRL GTVSKVPFFA PNMRQTFNDD YRIPVLIRIE PER LKMQLG ENADVVEHLG ELLKRGLRGS LKTGNLVTGA LYVDLDFYPN TPAITGIREF NGYQIIPTVS GGLAQIQQRL MEAL DKINK L(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)

UniProtKB: Intermembrane transport protein PqiB

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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
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

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.96 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 36591
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)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-5uvn:
Structure of E. coli MCE protein PqiB, periplasmic domain

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