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- EMDB-11083: Cryo-EM structure of the Acinetobacter baumannii MlaBDEF complex -

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Basic information

Entry
Database: EMDB / ID: EMD-11083
TitleCryo-EM structure of the Acinetobacter baumannii MlaBDEF complex
Map datamap of the Acinetobacter baumannii MlaBDEF complex to 4.2 A
Sample
  • Complex: MlaBDEF
Function / homology
Function and homology information


phospholipid transporter activity / ATP-binding cassette (ABC) transporter complex / phospholipid binding / extracellular region / ATP binding / membrane
Similarity search - Function
Probable ABC transporter ATP-binding protein MlaF/Mkl / ABC transport permease subunit MlaE, Proteobacteria / ABC transporter permease MalE / Permease MlaE / STAS domain / Mce/MlaD / MlaD protein / STAS domain / STAS domain superfamily / ABC transporter ...Probable ABC transporter ATP-binding protein MlaF/Mkl / ABC transport permease subunit MlaE, Proteobacteria / ABC transporter permease MalE / Permease MlaE / STAS domain / Mce/MlaD / MlaD protein / STAS domain / STAS domain superfamily / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ABC transporter ATP-binding protein / ABC transporter periplasmic substrate-binding protein / Intermembrane phospholipid transport system permease protein MlaE / Anti-sigma factor antagonist
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.24 Å
AuthorsMann D / Bergeron JRC
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R019061/1 United Kingdom
Citation
Journal: Commun Biol / Year: 2021
Title: Structure and lipid dynamics in the maintenance of lipid asymmetry inner membrane complex of A. baumannii.
Authors: Daniel Mann / Junping Fan / Kamolrat Somboon / Daniel P Farrell / Andrew Muenks / Svetomir B Tzokov / Frank DiMaio / Syma Khalid / Samuel I Miller / Julien R C Bergeron /
Abstract: Multi-resistant bacteria are a major threat in modern medicine. The gram-negative coccobacillus Acinetobacter baumannii currently leads the WHO list of pathogens in critical need for new therapeutic ...Multi-resistant bacteria are a major threat in modern medicine. The gram-negative coccobacillus Acinetobacter baumannii currently leads the WHO list of pathogens in critical need for new therapeutic development. The maintenance of lipid asymmetry (MLA) protein complex is one of the core machineries that transport lipids from/to the outer membrane in gram-negative bacteria. It also contributes to broad-range antibiotic resistance in several pathogens, most prominently in A. baumannii. Nonetheless, the molecular details of its role in lipid transport has remained largely elusive. Here, we report the cryo-EM maps of the core MLA complex, MlaBDEF, from the pathogen A. baumannii, in the apo-, ATP- and ADP-bound states, revealing multiple lipid binding sites in the cytosolic and periplasmic side of the complex. Molecular dynamics simulations suggest their potential trajectory across the membrane. Collectively with the recently-reported structures of the E. coli orthologue, this data also allows us to propose a molecular mechanism of lipid transport by the MLA system.
#1: Journal: Biorxiv / Year: 2020
Title: Structure and lipid dynamics in the A. baumannii maintenance of lipid asymmetry (MLA) inner membrane complex
Authors: Mann D / Fan J / Farrell DP / Somboon K / Muenks A / Tzokov SB / Khalid S / Dimaio F / Miller SI / Bergeron JRC
History
DepositionMay 27, 2020-
Header (metadata) releaseMay 5, 2021-
Map releaseMay 5, 2021-
UpdateJul 14, 2021-
Current statusJul 14, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0576
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0576
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11083.png

Downloads & links

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Map

FileDownload / File: emd_11083.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap of the Acinetobacter baumannii MlaBDEF complex to 4.2 A
Voxel sizeX=Y=Z: 0.82 Å
Density
Contour LevelBy AUTHOR: 0.0576 / Movie #1: 0.0576
Minimum - Maximum-0.06481779 - 0.16392095
Average (Standard dev.)0.0021562919 (±0.01102598)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 209.92 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.820.820.82
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z209.920209.920209.920
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0650.1640.002

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Supplemental data

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Sample components

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Entire : MlaBDEF

EntireName: MlaBDEF
Components
  • Complex: MlaBDEF

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Supramolecule #1: MlaBDEF

SupramoleculeName: MlaBDEF / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Acinetobacter baumannii (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.24 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 28699
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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