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- EMDB-11082: Cryo-EM structure of the A. baumannii MlaBDEF complex bound to APPNHP -

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Basic information

Entry
Database: EMDB / ID: EMD-11082
TitleCryo-EM structure of the A. baumannii MlaBDEF complex bound to APPNHP
Map dataMap of the A. baumannii MlaBDEF complex, bound to APPNHP, at 3.9A resolution.
Sample
  • Complex: MlaBDEF complex
    • Protein or peptide: ABC transporter permease
    • Protein or peptide: Anti-sigma factor antagonist
    • Protein or peptide: MCE family protein
    • Protein or peptide: ABC transporter ATP-binding protein
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
Keywordslipid transport / antibiotic resistance / ABC transporter / MEMBRANE PROTEIN
Function / homology
Function and homology information


ATP-binding cassette (ABC) transporter complex / 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: 3.9 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-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.458
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.458
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6z5u
  • Surface level: 0.458
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11082.png

Downloads & links

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Map

FileDownload / File: emd_11082.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of the A. baumannii MlaBDEF complex, bound to APPNHP, at 3.9A resolution.
Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 0.458 / Movie #1: 0.458
Minimum - Maximum-2.039904 - 3.099986
Average (Standard dev.)0.0065899994 (±0.0891228)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 273.92 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z273.920273.920273.920
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-2.0403.1000.007

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Supplemental data

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Mask #1

Fileemd_11082_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : MlaBDEF complex

EntireName: MlaBDEF complex
Components
  • Complex: MlaBDEF complex
    • Protein or peptide: ABC transporter permease
    • Protein or peptide: Anti-sigma factor antagonist
    • Protein or peptide: MCE family protein
    • Protein or peptide: ABC transporter ATP-binding protein
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION

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Supramolecule #1: MlaBDEF complex

SupramoleculeName: MlaBDEF complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Acinetobacter baumannii (bacteria)

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Macromolecule #1: ABC transporter permease

MacromoleculeName: ABC transporter permease / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (bacteria)
Molecular weightTheoretical: 27.322443 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNTIAWLGRL VIERIRGIGV AALMLLQIIF SLPSAGGFGR FVYQMHRVGV MSLLIITVSG LFIGLVLGLQ GYSILVNVGS ESMLGTMVS LTLLRELAPV VAALLFAGRA GSALTAEIGS MKQSEQLASM EMIGVDPLKQ IVSPRLWAGI VSLPMLTVIF A AIGIVGGK ...String:
MNTIAWLGRL VIERIRGIGV AALMLLQIIF SLPSAGGFGR FVYQMHRVGV MSLLIITVSG LFIGLVLGLQ GYSILVNVGS ESMLGTMVS LTLLRELAPV VAALLFAGRA GSALTAEIGS MKQSEQLASM EMIGVDPLKQ IVSPRLWAGI VSLPMLTVIF A AIGIVGGK LVGVDFLGVD EGSFWSGMQN NVQFGHDVVN GIIKSIVFAL LCTWIAVFQG YACDPTPEGI ATAMTRTVVY SS LCVLGFD FVLTAVMFGG I

UniProtKB: Intermembrane phospholipid transport system permease protein MlaE

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Macromolecule #2: Anti-sigma factor antagonist

MacromoleculeName: Anti-sigma factor antagonist / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (bacteria)
Molecular weightTheoretical: 10.874672 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MVQYLNQELV VSGKIDFENA EQQYQAGLAI IKKQTSFPLI VDLKQLEHGN TLALAVLVQW LRQTPQKSGL HFKNVPEKML KIIQACHLQ EDLHLV

UniProtKB: Anti-sigma factor antagonist

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Macromolecule #3: MCE family protein

MacromoleculeName: MCE family protein / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (bacteria)
Molecular weightTheoretical: 24.135322 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKSRTSELAV GIFVIIFGIA LFFLAMKVSG LVGTNLSDGY TMKAQFDNVN GLKPRAKVTM SGVTIGRVDS ITLDPVTRLA TVTFDLDGK LTSFNAEQLK EVQKNALDEL RYSSDYTQAT PAQQKTMEQQ LISNMNSITS IDEDAYIMVA TNGLLGEKYL K IVPGGGLN ...String:
MKSRTSELAV GIFVIIFGIA LFFLAMKVSG LVGTNLSDGY TMKAQFDNVN GLKPRAKVTM SGVTIGRVDS ITLDPVTRLA TVTFDLDGK LTSFNAEQLK EVQKNALDEL RYSSDYTQAT PAQQKTMEQQ LISNMNSITS IDEDAYIMVA TNGLLGEKYL K IVPGGGLN YLKRGDTISN TQGTMDLEDL ISKFITGGGA GKVAAGSSSA EEKAPASTDS SAQPSFVE

UniProtKB: ABC transporter periplasmic substrate-binding protein

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Macromolecule #4: ABC transporter ATP-binding protein

MacromoleculeName: ABC transporter ATP-binding protein / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (bacteria)
Molecular weightTheoretical: 30.367848 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MIAIMNNKTP LSTQSLIEVK NLSFNRGERV IYDNISLNIR RGQITAIMGP SGTGKTTLLR LIGGQLVPDQ GEVLLDGKDI AQMSRQELF AARARMGMLF QSGALFTDMS VYENVAFPIR AHTKLSENLI AELVALKLES VGLRGTEQLM PTELSGGMNR R VALARAIA ...String:
MIAIMNNKTP LSTQSLIEVK NLSFNRGERV IYDNISLNIR RGQITAIMGP SGTGKTTLLR LIGGQLVPDQ GEVLLDGKDI AQMSRQELF AARARMGMLF QSGALFTDMS VYENVAFPIR AHTKLSENLI AELVALKLES VGLRGTEQLM PTELSGGMNR R VALARAIA LDPDLIMYDE PFAGQDPIVK GVLTRLIRSL REALDLTTII VSHDVPETLS IADYIYVVAE GKIQGEGTPE EL QAYASPF VKQFLTGSAE GPVEYQFSHQ AYLDNEVRP

UniProtKB: ABC transporter ATP-binding protein

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Macromolecule #5: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 5 / Number of copies: 2 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

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Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 47.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 93295

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