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- EMDB-25400: Multidrug efflux pump subunit AcrB -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-25400
TitleMultidrug efflux pump subunit AcrB
Map data
Sample
  • Complex: Multidrug efflux pump subunit AcrB
    • Protein or peptide: Multidrug efflux pump subunit AcrB
KeywordsMultidrug efflux pump subunit AcrB / NCMN / 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 / 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 (strain K12) (bacteria) / Escherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 3.69 Å
AuthorsTrinh TKH / Catalano C / Guo Y
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM132329 United States
CitationJournal: Nanoscale Adv / Year: 2023
Title: Fabrication of membrane proteins in the form of native cell membrane nanoparticles using novel membrane active polymers.
Authors: Thi Kim Hoang Trinh / Claudio Catalano / Youzhong Guo /
Abstract: Membrane proteins are a widespread class of bio-macromolecules responsible for numerous vital biological processes and serve as therapeutic targets for a vast array of contemporary medications. For ...Membrane proteins are a widespread class of bio-macromolecules responsible for numerous vital biological processes and serve as therapeutic targets for a vast array of contemporary medications. For membrane protein isolation and purification, detergents have historically been used. Despite this, detergents frequently result in protein instability. Consequently, their application was limited. Recent detergent-free approaches have been invented. Among these, styrene-maleic acid lipid particle (SMALP), diisobutylene-maleic acid lipid particle (DIBMALP), and native cell membrane nanoparticle (NCMN) systems are the most prevalent. The NCMN system intends to create a library of membrane-active polymers suitable for high-resolution structure determination of membrane protein. Design, synthesis, characterization, and comparative application evaluations of three novel classes of NCMN polymers, NCMNP13-, NCMNP21-, and NCMNP21b-, are presented in this article. Although each NCMN polymer can solubilize distinct model membrane proteins and retain native lipids in NCMN particles, only the NCMNP21b- family produces lipid-protein particles with ideal buffer compatibility and high homogeneity suitable for single-particle cryo-EM analysis. NCMNP21b- polymers that generate high-quality NCMN particles are particularly desirable for membrane protein structural biology.
History
DepositionNov 8, 2021-
Header (metadata) releaseNov 23, 2022-
Map releaseNov 23, 2022-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25400.png

Downloads & links

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Map

FileDownload / File: emd_25400.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 360 pix.
= 297.216 Å		0.83 Å/pix.
x 360 pix.
= 297.216 Å		0.83 Å/pix.
x 360 pix.
= 297.216 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8256 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.305
Minimum - Maximum-1.217363 - 1.8516966
Average (Standard dev.)0.003064855 (±0.05483498)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 297.216 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Multidrug efflux pump subunit AcrB

EntireName: Multidrug efflux pump subunit AcrB
Components
  • Complex: Multidrug efflux pump subunit AcrB
    • Protein or peptide: Multidrug efflux pump subunit AcrB

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Supramolecule #1: Multidrug efflux pump subunit AcrB

SupramoleculeName: Multidrug efflux pump subunit AcrB / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (strain K12) (bacteria)

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Macromolecule #1: Multidrug efflux pump subunit AcrB

MacromoleculeName: Multidrug efflux pump subunit AcrB / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MPNFFIDRPI FAWVIAIIIM LAGGLAILKL PVAQYPTIAP PAVTISASYP GADAKTVQDT VTQVIEQNM NGIDNLMYMS SNSDSTGTVQ ITLTFESGTD ADIAQVQVQN KLQLAMPLLP Q EVQQQGVS VEKSSSSFLM VVGVINTDGT MTQEDISDYV AANMKDAISR ...String:
MPNFFIDRPI FAWVIAIIIM LAGGLAILKL PVAQYPTIAP PAVTISASYP GADAKTVQDT VTQVIEQNM NGIDNLMYMS SNSDSTGTVQ ITLTFESGTD ADIAQVQVQN KLQLAMPLLP Q EVQQQGVS VEKSSSSFLM VVGVINTDGT MTQEDISDYV AANMKDAISR TSGVGDVQLF GS QYAMRIW MNPNELNKFQ LTPVDVITAI KAQNAQVAAG QLGGTPPVKG QQLNASIIAQ TRL TSTEEF GKILLKVNQD GSRVLLRDVA KIELGGENYD IIAEFNGQPA SGLGIKLATG ANAL DTAAA IRAELAKMEP FFPSGLKIVY PYDTTPFVKI SIHEVVKTLV EAIILVFLVM YLFLQ NFRA TLIPTIAVPV VLLGTFAVLA AFGFSINTLT MFGMVLAIGL LVDDAIVVVE NVERVM AEE GLPPKEATRK SMGQIQGALV GIAMVLSAVF VPMAFFGGST GAIYRQFSIT IVSAMAL SV LVALILTPAL CATMLKPIAK GDHGEGKKGF FGWFNRMFEK STHHYTDSVG GILRSTGR Y LVLYLIIVVG MAYLFVRLPS SFLPDEDQGV FMTMVQLPAG ATQERTQKVL NEVTHYYLT KEKNNVESVF AVNGFGFAGR GQNTGIAFVS LKDWADRPGE ENKVEAITMR ATRAFSQIKD AMVFAFNLP AIVELGTATG FDFELIDQAG LGHEKLTQAR NQLLAEAAKH PDMLTSVRPN G LEDTPQFK IDIDQEKAQA LGVSINDINT TLGAAWGGSY VNDFIDRGRV KKVYVMSEAK YR MLPDDIG DWYVRAADGQ MVPFSAFSSS RWEYGSPRLE RYNGLPSMEI LGQAAPGKST GEA MELMEQ LASKLPTGVG YDWTGMSYQE RLSGNQAPSL YAISLIVVFL CLAALYESWS IPFS VMLVV PLGVIGALLA ATFRGLTNDV YFQVGLLTTI GLSAKNAILI VEFAKDLMDK EGKGL IEAT LDAVRMRLRP ILMTSLAFIL GVMPLVISTG AGSGAQNAVG TGVMGGMVTA TVLAIF FVP VFFVVVRRRF SRKNEDIEHS HTVDHH

UniProtKB: Multidrug efflux pump subunit AcrB

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.8
StainingType: NEGATIVE / Material: 2% uranyl acetate
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 44.18 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: RANDOM CONICAL TILT
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.69 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 86011
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER

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