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- PDB-9fe4: Crystallographic structure of AcrB V612F -

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Basic information

Entry
Database: PDB / ID: 9fe4
TitleCrystallographic structure of AcrB V612F
ComponentsMultidrug efflux pump subunit AcrB
KeywordsTRANSPORT PROTEIN / Drug efflux / RND transporter
Function / homology
Function and homology information


alkane transmembrane transporter activity / alkane transport / enterobactin transport / enterobactin transmembrane transporter activity / xenobiotic detoxification by transmembrane export across the cell outer membrane / periplasmic side of plasma membrane / efflux pump complex / bile acid transmembrane transporter activity / xenobiotic transport / bile acid and bile salt transport ...alkane transmembrane transporter activity / alkane transport / enterobactin transport / enterobactin transmembrane transporter activity / xenobiotic detoxification by transmembrane export across the cell outer membrane / periplasmic side of plasma membrane / efflux pump complex / bile acid transmembrane transporter activity / xenobiotic transport / bile acid and bile salt transport / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / fatty acid transport / response to toxic substance / response to xenobiotic stimulus / response to antibiotic / identical protein binding / membrane / plasma membrane
Similarity search - Function
Hydrophobe/amphiphile efflux-1 HAE1 / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / Acriflavin resistance protein / AcrB/AcrD/AcrF family
Similarity search - Domain/homology
Multidrug efflux pump subunit AcrB
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLazarova, M. / Diederichs, K. / Pos, K.M.
Funding support Switzerland, Germany, 4items
OrganizationGrant numberCountry
Swiss National Science Foundation3100A0_118402 Switzerland
German Research Foundation (DFG)SFB807-P18 Germany
German Research Foundation (DFG)SFB1507-P3 Germany
German Research Foundation (DFG)DFG-EXC115 Germany
CitationJournal: Nat Commun / Year: 2025
Title: Conformational plasticity across phylogenetic clusters of RND multidrug efflux pumps and its impact on substrate specificity.
Authors: Mariya Lazarova / Thomas Eicher / Clara Börnsen / Hui Zeng / Mohd Athar / Ui Okada / Eiki Yamashita / Inga M Spannaus / Max Borgosch / Hi-Jea Cha / Attilio V Vargiu / Satoshi Murakami / Kay ...Authors: Mariya Lazarova / Thomas Eicher / Clara Börnsen / Hui Zeng / Mohd Athar / Ui Okada / Eiki Yamashita / Inga M Spannaus / Max Borgosch / Hi-Jea Cha / Attilio V Vargiu / Satoshi Murakami / Kay Diederichs / Achilleas S Frangakis / Klaas M Pos /
Abstract: Antibiotic efflux plays a key role for the multidrug resistance in Gram-negative bacteria. Multidrug efflux pumps of the resistance nodulation and cell division (RND) superfamily function as part of ...Antibiotic efflux plays a key role for the multidrug resistance in Gram-negative bacteria. Multidrug efflux pumps of the resistance nodulation and cell division (RND) superfamily function as part of cell envelope spanning systems and provide resistance to diverse antibiotics. Here, we identify two phylogenetic clusters of RND proteins with conserved binding pocket residues and show that the transfer of a single conserved residue between both clusters affects the resistance phenotype not only due to changes in the physicochemical properties of the binding pocket, but also due to an altered equilibrium between the conformational states of the transport cycle. We demonstrate, using single-particle cryo-electron microscopy, that AcrB and OqxB, which represent both clusters, adopt fundamentally different apo states, implying distinct mechanisms for initial substrate binding. The observed conformational plasticity appears phylogenetically conserved and likely plays a role in the diversification of the resistance phenotype among homologous RND pumps.
History
DepositionMay 17, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 28, 2025Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Multidrug efflux pump subunit AcrB


Theoretical massNumber of molelcules
Total (without water)114,7841
Polymers114,7841
Non-polymers00
Water00
1
B: Multidrug efflux pump subunit AcrB

B: Multidrug efflux pump subunit AcrB

B: Multidrug efflux pump subunit AcrB


Theoretical massNumber of molelcules
Total (without water)344,3533
Polymers344,3533
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area18480 Å2
ΔGint-74 kcal/mol
Surface area116580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.410, 134.410, 190.970
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein Multidrug efflux pump subunit AcrB / AcrAB-TolC multidrug efflux pump subunit AcrB / Acridine resistance protein B


Mass: 114784.336 Da / Num. of mol.: 1 / Mutation: V612F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: acrB, acrE, b0462, JW0451 / Production host: Escherichia coli (E. coli) / References: UniProt: P31224
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.34 Å3/Da / Density % sol: 71.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1M citrate pH 4.6, 5% PEG400, 16-21% PEG300, 8-11% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 22, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→49.7 Å / Num. obs: 49616 / % possible obs: 99.73 % / Redundancy: 11 % / CC1/2: 0.999 / Net I/σ(I): 20.19
Reflection shellResolution: 2.8→2.9 Å / Num. unique obs: 4859 / CC1/2: 0.335

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Processing

Software
NameVersionClassification
PHENIX1.20.1refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→49.7 Å / Cross valid method: FREE R-VALUE / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3004 2481 -
Rwork0.2585 --
obs-49616 99.76 %
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→49.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7843 0 0 0 7843
LS refinement shellResolution: 2.8→2.85 Å

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