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- EMDB-2044: Electron microscopy of Aa MacA-MexA alpha;-hybrid and Aa MacA-Opr... -

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Basic information

Entry
Database: EMDB / ID: EMD-2044
TitleElectron microscopy of Aa MacA-MexA alpha;-hybrid and Aa MacA-OprM alpha;-hybrid- dimer
Map dataAa MacA-MexAα-hybrid and Aa MacA-OprMα-hybrid- dimer
Sample
  • Sample: Aa MacA-MexAα-hybrid and Aa MacA-OprMα-hybrid- dimer
  • Protein or peptide: Aa MacA-MexAα-hybrid and Aa MacA-OprMα-hybrid- dimer
KeywordsBacterial pathogenesis / Multidrug resistance / MexA / OprM / TolC
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / Resolution: 24.0 Å
AuthorsXu Y / Moeller A / So-Young J / Minho L / Bo-Young Y / Jin-Sik K / Lee K / Ha NC
CitationJournal: J Biol Chem / Year: 2012
Title: Assembly and channel opening of outer membrane protein in tripartite drug efflux pumps of Gram-negative bacteria.
Authors: Yongbin Xu / Arne Moeller / So-Young Jun / Minho Le / Bo-Young Yoon / Jin-Sik Kim / Kangseok Lee / Nam-Chul Ha /
Abstract: Gram-negative bacteria are capable of expelling diverse xenobiotic substances from within the cell by use of three-component efflux pumps in which the energy-activated inner membrane transporter is ...Gram-negative bacteria are capable of expelling diverse xenobiotic substances from within the cell by use of three-component efflux pumps in which the energy-activated inner membrane transporter is connected to the outer membrane channel protein via the membrane fusion protein. In this work, we describe the crystal structure of the membrane fusion protein MexA from the Pseudomonas aeruginosa MexAB-OprM pump in the hexameric ring arrangement. Electron microscopy study on the chimeric complex of MexA and the outer membrane protein OprM reveals that MexA makes a tip-to-tip interaction with OprM, which suggests a docking model for MexA and OprM. This docking model agrees well with genetic results and depicts detailed interactions. Opening of the OprM channel is accompanied by the simultaneous exposure of a protein structure resembling a six-bladed cogwheel, which intermeshes with the complementary cogwheel structure in the MexA hexamer. Taken together, we suggest an assembly and channel opening model for the MexAB-OprM pump. This study provides a better understanding of multidrug resistance in Gram-negative bacteria.
History
DepositionFeb 8, 2012-
Header (metadata) releaseSep 26, 2012-
Map releaseSep 26, 2012-
UpdateDec 11, 2013-
Current statusDec 11, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2044.jpg

Downloads & links

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Map

FileDownload / File: emd_2044.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAa MacA-MexAα-hybrid and Aa MacA-OprMα-hybrid- dimer
Voxel sizeX=Y=Z: 2.17 Å
Density
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.02051534 - 0.03351603
Average (Standard dev.)0.00132435 (±0.00292133)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-100-100-100
Dimensions200200200
Spacing200200200
CellA=B=C: 434.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.172.172.17
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z434.000434.000434.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS-100-100-100
NC/NR/NS200200200
D min/max/mean-0.0210.0340.001

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Supplemental data

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Sample components

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Entire : Aa MacA-MexAα-hybrid and Aa MacA-OprMα-hybrid- dimer

EntireName: Aa MacA-MexAα-hybrid and Aa MacA-OprMα-hybrid- dimer
Components
  • Sample: Aa MacA-MexAα-hybrid and Aa MacA-OprMα-hybrid- dimer
  • Protein or peptide: Aa MacA-MexAα-hybrid and Aa MacA-OprMα-hybrid- dimer

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Supramolecule #1000: Aa MacA-MexAα-hybrid and Aa MacA-OprMα-hybrid- dimer

SupramoleculeName: Aa MacA-MexAα-hybrid and Aa MacA-OprMα-hybrid- dimer
type: sample / ID: 1000 / Oligomeric state: hexamer / Number unique components: 1

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Macromolecule #1: Aa MacA-MexAα-hybrid and Aa MacA-OprMα-hybrid- dimer

MacromoleculeName: Aa MacA-MexAα-hybrid and Aa MacA-OprMα-hybrid- dimer
type: protein_or_peptide / ID: 1 / Recombinant expression: Yes
Source (natural)Organism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC
DateAug 4, 2011
Image recordingNumber real images: 1441 / Average electron dose: 45 e/Å2
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 24.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 2244

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