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- EMDB-52452: Structure of the co-purified multidrug transporter subunit ACRB i... -

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Basic information

Entry
Database: EMDB / ID: EMD-52452
TitleStructure of the co-purified multidrug transporter subunit ACRB in nandisc
Map dataUnsharpened map
Sample
  • Complex: Trimeric complex of ACRB transporter co-purified from E.coli in nanodisc
    • Protein or peptide: Multidrug efflux pump subunit AcrB
KeywordsMultidrug transporter / TRANSPORT PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.27 Å
AuthorsMim C / Zhang Q / Murthy AV
Funding support Sweden, 1 items
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, 2025-
Header (metadata) releaseJan 14, 2026-
Map releaseJan 14, 2026-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52452.png

Downloads & links

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Map

FileDownload / File: emd_52452.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened map
Voxel sizeX=Y=Z: 0.66 Å
Density
Contour LevelBy AUTHOR: 0.01589
Minimum - Maximum-0.032565415 - 0.07001712
Average (Standard dev.)0.00018116593 (±0.0039529507)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 237.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52452_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Additional map: 3DVA cluster 3

Fileemd_52452_additional_1.map
Annotation3DVA cluster 3
Projections & Slices
AxesZYX

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Additional map: 3DVA cluster 1

Fileemd_52452_additional_2.map
Annotation3DVA cluster 1
Projections & Slices
AxesZYX

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Additional map: 3DVA cluster 2

Fileemd_52452_additional_3.map
Annotation3DVA cluster 2
Projections & Slices
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Additional map: 3DVA cluster 0

Fileemd_52452_additional_4.map
Annotation3DVA cluster 0
Projections & Slices
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Additional map: Sharpened with DeepEMhancer

Fileemd_52452_additional_5.map
AnnotationSharpened with DeepEMhancer
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Half map: #2

Fileemd_52452_half_map_1.map
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Half map: #1

Fileemd_52452_half_map_2.map
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Sample components

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Entire : Trimeric complex of ACRB transporter co-purified from E.coli in n...

EntireName: Trimeric complex of ACRB transporter co-purified from E.coli in nanodisc
Components
  • Complex: Trimeric complex of ACRB transporter co-purified from E.coli in nanodisc
    • Protein or peptide: Multidrug efflux pump subunit AcrB

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Supramolecule #1: Trimeric complex of ACRB transporter co-purified from E.coli in n...

SupramoleculeName: Trimeric complex of ACRB transporter co-purified from E.coli in nanodisc
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Multidrug efflux pump subunit AcrB

MacromoleculeName: Multidrug efflux pump subunit AcrB / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 113.66518 KDa
SequenceString: MPNFFIDRPI FAWVIAIIIM LAGGLAILKL PVAQYPTIAP PAVTISASYP GADAKTVQDT VTQVIEQNMN GIDNLMYMSS NSDSTGTVQ ITLTFESGTD ADIAQVQVQN KLQLAMPLLP QEVQQQGVSV EKSSSSFLMV VGVINTDGTM TQEDISDYVA A NMKDAISR ...String:
MPNFFIDRPI FAWVIAIIIM LAGGLAILKL PVAQYPTIAP PAVTISASYP GADAKTVQDT VTQVIEQNMN GIDNLMYMSS NSDSTGTVQ ITLTFESGTD ADIAQVQVQN KLQLAMPLLP QEVQQQGVSV EKSSSSFLMV VGVINTDGTM TQEDISDYVA A NMKDAISR TSGVGDVQLF GSQYAMRIWM NPNELNKFQL TPVDVITAIK AQNAQVAAGQ LGGTPPVKGQ QLNASIIAQT RL TSTEEFG KILLKVNQDG SRVLLRDVAK IELGGENYDI IAEFNGQPAS GLGIKLATGA NALDTAAAIR AELAKMEPFF PSG LKIVYP YDTTPFVKIS IHEVVKTLVE AIILVFLVMY LFLQNFRATL IPTIAVPVVL LGTFAVLAAF GFSINTLTMF GMVL AIGLL VDDAIVVVEN VERVMAEEGL PPKEATRKSM GQIQGALVGI AMVLSAVFVP MAFFGGSTGA IYRQFSITIV SAMAL SVLV ALILTPALCA TMLKPIAKGD HGEGKKGFFG WFNRMFEKST HHYTDSVGGI LRSTGRYLVL YLIIVVGMAY LFVRLP SSF LPDEDQGVFM TMVQLPAGAT QERTQKVLNE VTHYYLTKEK NNVESVFAVN GFGFAGRGQN TGIAFVSLKD WADRPGE EN KVEAITMRAT RAFSQIKDAM VFAFNLPAIV ELGTATGFDF ELIDQAGLGH EKLTQARNQL LAEAAKHPDM LTSVRPNG L EDTPQFKIDI DQEKAQALGV SINDINTTLG AAWGGSYVND FIDRGRVKKV YVMSEAKYRM LPDDIGDWYV RAADGQMVP FSAFSSSRWE YGSPRLERYN GLPSMEILGQ AAPGKSTGEA MELMEQLASK LPTGVGYDWT GMSYQERLSG NQAPSLYAIS LIVVFLCLA ALYESWSIPF SVMLVVPLGV IGALLAATFR GLTNDVYFQV GLLTTIGLSA KNAILIVEFA KDLMDKEGKG L IEATLDAV RMRLRPILMT SLAFILGVMP LVISTGAGSG AQNAVGTGVM GGMVTATVLA IFFVPVFFVV VRRRFSRKNE DI EHSHTVD HH

UniProtKB: Multidrug efflux pump subunit AcrB

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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

Concentration4.6 mg/mL
BufferpH: 7.5 / Details: 50mM HEPES, 150mM NaCl and 5mM EGTA
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Details: 20mA
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV / Details: 100% humidity, 16C.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 82720
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial modelPDB ID:

2hrt


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: BACKBONE TRACE
Output model

PDB-9hwl:
Structure of the co-purified multidrug transporter subunit ACRB in nandisc

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