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- PDB-9hwl: Structure of the co-purified multidrug transporter subunit ACRB i... -

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Basic information

Entry
Database: PDB / ID: 9hwl
TitleStructure of the co-purified multidrug transporter subunit ACRB in nandisc
ComponentsMultidrug efflux pump subunit AcrB
KeywordsTRANSPORT PROTEIN / Multidrug 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 / Iron assimilation using enterobactin / bile acid transmembrane transporter activity / Antimicrobial resistance ...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 / Iron assimilation using enterobactin / bile acid transmembrane transporter activity / Antimicrobial resistance / bile acid and bile salt transport / Secretion of toxins / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / fatty acid transport / xenobiotic transport / response to toxic substance / response to xenobiotic stimulus / response to antibiotic / membrane / identical protein binding / 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 (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.27 Å
AuthorsMim, C. / Zhang, Q. / Murthy, A.V.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Carl Trygger FoundationCTS 21:1630 Sweden
CitationJournal: PLoS One / Year: 2026
Title: Exploration of a workflow for the classification and identification of co-purified protein complexes yields new structures and multiple MSP assembly states.
Authors: Qingyang Zhang / Abhinandan Venkatesha Murthy / Carsten Mim /
Abstract: Native protein complexes have garnered interest as targets for structural dissemination. Cryogenic electron microscopy (cryo-EM) with its ability to image protein mixtures is the most promising tool ...Native protein complexes have garnered interest as targets for structural dissemination. Cryogenic electron microscopy (cryo-EM) with its ability to image protein mixtures is the most promising tool to enable structural proteomics. Additionally, image processing has evolved and can deal with conformational and compositional heterogeneity. Integrative approaches, namely mass spectrometry in conjunction with cryo-EM, have made it possible to characterize and identify complex mixtures. However, this comes at a cost of generating models and interpreting mass spectra. Here we present a modified approach that builds on publicly available software. By generating maps around 4 Å and unsupervised model building we were able to identify the most abundant proteins in our sample. This sample consisted of co-purified membrane proteins in nanodiscs. We found a novel structure and unexpected nanodisc assemblies. Our maps imply a direct interaction between membrane proteins and membrane scaffolding proteins.
History
DepositionJan 5, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 14, 2026Provider: repository / Type: Initial release
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Revision 1.0Jan 14, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
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Revision 1.0Jan 14, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Multidrug efflux pump subunit AcrB
B: Multidrug efflux pump subunit AcrB
C: Multidrug efflux pump subunit AcrB


Theoretical massNumber of molelcules
Total (without water)340,9963
Polymers340,9963
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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


Mass: 113665.180 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P31224
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Trimeric complex of ACRB transporter co-purified from E.coli in nanodisc
Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5 / Details: 50mM HEPES, 150mM NaCl and 5mM EGTA
SpecimenConc.: 4.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 20mA / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Details: 100% humidity, 16C

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
4cryoSPARCCTF correction
7ISOLDEmodel fitting
9cryoSPARCinitial Euler assignment
12cryoSPARC3D reconstruction
13PHENIXdev_5510model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 82720 / Symmetry type: POINT
Atomic model buildingProtocol: BACKBONE TRACE
Atomic model buildingPDB-ID: 2hrt

2hrt


Accession code: 2hrt / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 167.25 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.010224025
ELECTRON MICROSCOPYf_angle_d0.862632622
ELECTRON MICROSCOPYf_chiral_restr0.05163840
ELECTRON MICROSCOPYf_plane_restr0.00764173
ELECTRON MICROSCOPYf_dihedral_angle_d12.31428686

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