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- EMDB-22867: Cryo-EM Structures of AdeB from Acinetobacter baumannii: AdeB-II -

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Basic information

Entry
Database: EMDB / ID: EMD-22867
TitleCryo-EM Structures of AdeB from Acinetobacter baumannii: AdeB-II
Map dataDensity modified map of AdeB-II
Sample
  • Complex: AdeB
    • Protein or peptide: Efflux pump membrane transporter
  • Ligand: PHOSPHATIDYLETHANOLAMINE
KeywordsAdeB / Acinetobacter baumannii / Membrane Protein / Cryo-EM / RND transporter / TRANSPORT PROTEIN
Function / homologyHydrophobe/amphiphile efflux-1 HAE1 / Acriflavin resistance protein / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / AcrB/AcrD/AcrF family / xenobiotic transport / efflux transmembrane transporter activity / plasma membrane / Efflux pump membrane transporter
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.21 Å
AuthorsMorgan CE / Yu EW
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: mBio / Year: 2021
Title: Cryoelectron Microscopy Structures of AdeB Illuminate Mechanisms of Simultaneous Binding and Exporting of Substrates.
Authors: Christopher E Morgan / Przemyslaw Glaza / Inga V Leus / Anhthu Trinh / Chih-Chia Su / Meng Cui / Helen I Zgurskaya / Edward W Yu /
Abstract: is a Gram-negative pathogen that has emerged as one of the most highly antibiotic-resistant bacteria worldwide. Multidrug efflux within these highly drug-resistant strains and other opportunistic ... is a Gram-negative pathogen that has emerged as one of the most highly antibiotic-resistant bacteria worldwide. Multidrug efflux within these highly drug-resistant strains and other opportunistic pathogens is a major cause of failure of drug-based treatments of infectious diseases. The best-characterized multidrug efflux system in is the prevalent rug fflux B (AdeB) pump, which is a member of the resistance-nodulation-cell division (RND) superfamily. Here, we report six structures of the trimeric AdeB multidrug efflux pump in the presence of ethidium bromide using single-particle cryoelectron microscopy (cryo-EM). These structures allow us to directly observe various novel conformational states of the AdeB trimer, including the transmembrane region of trimeric AdeB can be associated with form a trimer assembly or dissociated into "dimer plus monomer" and "monomer plus monomer plus monomer" configurations. We also discover that a single AdeB protomer can simultaneously anchor a number of ethidium ligands and that different AdeB protomers can bind ethidium molecules simultaneously. Combined with molecular dynamics (MD) simulations, we reveal a drug transport mechanism that involves multiple multidrug-binding sites and various transient states of the AdeB membrane protein. Our data suggest that each AdeB protomer within the trimer binds and exports drugs independently. has emerged as one of the most highly antibiotic-resistant Gram-negative pathogens. The prevalent AdeB multidrug efflux pump mediates resistance to a broad spectrum of clinically relevant antimicrobial agents. Here, we report six cryo-EM structures of the trimeric AdeB pump in the presence of ethidium bromide. We discover that a single AdeB protomer can simultaneously anchor a number of ligands, and different AdeB protomers can bind ethidium molecules simultaneously. The results indicate that each AdeB protomer within the trimer recognizes and extrudes drugs independently.
History
DepositionOct 16, 2020-
Header (metadata) releaseMar 10, 2021-
Map releaseMar 10, 2021-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.2
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.2
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7kge
  • Surface level: 0.2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_22867.map.gz / Format: CCP4 / Size: 8.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDensity modified map of AdeB-II
Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 0.2 / Movie #1: 0.2
Minimum - Maximum-1.6475545 - 2.6066136
Average (Standard dev.)-0.000000000002353 (±0.18895833)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin11288112
Dimensions121146128
Spacing128121146
CellA: 138.24 Å / B: 130.68001 Å / C: 157.68001 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z128121146
origin x/y/z0.0000.0000.000
length x/y/z138.240130.680157.680
α/β/γ90.00090.00090.000
start NX/NY/NZ11211288
NX/NY/NZ128121146
MAP C/R/S321
start NC/NR/NS88112112
NC/NR/NS146121128
D min/max/mean-1.6482.607-0.000

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Supplemental data

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Sample components

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Entire : AdeB

EntireName: AdeB
Components
  • Complex: AdeB
    • Protein or peptide: Efflux pump membrane transporter
  • Ligand: PHOSPHATIDYLETHANOLAMINE

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Supramolecule #1: AdeB

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

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Macromolecule #1: Efflux pump membrane transporter

MacromoleculeName: Efflux pump membrane transporter / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (bacteria)
Molecular weightTheoretical: 112.588297 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSQFFIRRPV FAWVIAIFII IFGLLSIPKL PIARFPSVAP PQVNISATYP GATAKTINDS VVTLIERELS GVKNLLYYSA TTDTSGTAE ITATFKPGTD VEMAQVDVQN KIKAVEARLP QVVRQQGLQV EASSSGFLML VGINSPNNQY SEVDLSDYLV R NVVEELKR ...String:
MSQFFIRRPV FAWVIAIFII IFGLLSIPKL PIARFPSVAP PQVNISATYP GATAKTINDS VVTLIERELS GVKNLLYYSA TTDTSGTAE ITATFKPGTD VEMAQVDVQN KIKAVEARLP QVVRQQGLQV EASSSGFLML VGINSPNNQY SEVDLSDYLV R NVVEELKR VEGVGKVQSF GAEKAMRIWV DPNKLVSYGL SISDVNNAIR ENNVEIAPGR LGDLPAEKGQ LITIPLSAQG QL SSLEQFK NISLKSKTNG SVIKLSDVAN VEIGSQAYNF AILENGKPAT AAAIQLSPGA NAVKTAEGVR AKIEELKLNL PEG MEFSIP YDTAPFVKIS IEKVIHTLLE AMVLVFIVMY LFLHNVRYTL IPAIVAPIAL LGTFTVMLLA GFSINVLTMF GMVL AIGII VDDAIVVVEN VERIMATEGL SPKDATSKAM KEITSPIIGI TLVLAAVFLP MAFASGSVGV IYKQFTLTMS VSILF SALL ALILTPALCA TILKPIDGHH QKKGFFAWFD RSFDKVTKKY ELMLLKIIKH TVPMMVIFLV ITGITFAGMK YWPTAF MPE EDQGWFMTSF QLPSDATAER TRNVVNQFEN NLKDNPDVKS NTAILGWGFS GAGQNVAVAF TTLKDFKERT SSASKMT SD VNSSMANSTE GETMAVLPPA IDELGTFSGF SLRLQDRANL GMPALLAAQD ELMAMAAKNK KFYMVWNEGL PQGDNISL K IDREKLSALG VKFSDVSDII STSMGSMYIN DFPNQGRMQQ VIVQVEAKSR MQLKDILNLK VMGSSGQLVS LSEVVTPQW NKAPQQYNRY NGRPSLSIAG IPNFDTSSGE AMREMEQLIA KLPKGIGYEW TGISLQEKQS ESQMAFLLGL SMLVVFLVLA ALYESWAIP LSVMLVVPLG IFGAIIAIMS RGLMNDVFFK IGLITIIGLS AKNAILIVEF AKMLKEEGMS LIEATVAAAK L RLRPILMT SLAFTCGVIP LVIATGASSE TQHALGTGVF GGMISATILA IFFVPVFFIF ILGAVEKLFS SKKKISS

UniProtKB: Efflux pump membrane transporter

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Macromolecule #2: PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 2 / Number of copies: 3 / Formula: PTY
Molecular weightTheoretical: 734.039 Da
Chemical component information

ChemComp-PTY:
PHOSPHATIDYLETHANOLAMINE / phospholipid*YM / Phosphatidylethanolamine

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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: 6.5
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 K3 (6k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 40.0 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 reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.15) / Number images used: 95552

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