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- EMDB-3653: Structure of the MacAB-TolC ABC-type tripartite multidrug efflux ... -

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Basic information

Entry
Database: EMDB / ID: EMD-3653
TitleStructure of the MacAB-TolC ABC-type tripartite multidrug efflux pump-MacB section
Map dataThe membrane proximal domain of MacA and MacB
Sample
  • Complex: MacAB-TolC
    • Protein or peptide: Outer membrane protein TolC
    • Protein or peptide: Macrolide export protein MacA
    • Protein or peptide: Macrolide export ATP-binding/permease protein MacB
Function / homology
Function and homology information


MacAB-TolC complex / enterobactin transport / bile acid transmembrane transporter activity / xenobiotic detoxification by transmembrane export across the cell outer membrane / efflux pump complex / periplasmic side of plasma membrane / xenobiotic detoxification by transmembrane export across the plasma membrane / bile acid and bile salt transport / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / ABC-type xenobiotic transporter activity ...MacAB-TolC complex / enterobactin transport / bile acid transmembrane transporter activity / xenobiotic detoxification by transmembrane export across the cell outer membrane / efflux pump complex / periplasmic side of plasma membrane / xenobiotic detoxification by transmembrane export across the plasma membrane / bile acid and bile salt transport / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / ABC-type xenobiotic transporter activity / extrinsic component of membrane / porin activity / efflux transmembrane transporter activity / transmembrane transporter activity / monoatomic ion transmembrane transport / cell outer membrane / response to organic cyclic compound / response to toxic substance / monoatomic ion channel activity / outer membrane-bounded periplasmic space / response to xenobiotic stimulus / response to antibiotic / ATP hydrolysis activity / protein homodimerization activity / ATP binding / membrane / identical protein binding / plasma membrane
Similarity search - Function
Macrolide export protein MacA / Macrolide export ATP-binding/permease protein macB family profile. / Type I secretion outer membrane protein, TolC / RND efflux pump, membrane fusion protein / RND efflux pump, membrane fusion protein, barrel-sandwich domain / MacB-like periplasmic core domain / MacB-like periplasmic core domain / Barrel-sandwich domain of CusB or HlyD membrane-fusion / Outer membrane efflux protein / Outer membrane efflux protein ...Macrolide export protein MacA / Macrolide export ATP-binding/permease protein macB family profile. / Type I secretion outer membrane protein, TolC / RND efflux pump, membrane fusion protein / RND efflux pump, membrane fusion protein, barrel-sandwich domain / MacB-like periplasmic core domain / MacB-like periplasmic core domain / Barrel-sandwich domain of CusB or HlyD membrane-fusion / Outer membrane efflux protein / Outer membrane efflux protein / MacB, ATP-binding domain / ABC3 transporter permease protein domain / FtsX-like permease family / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Outer membrane protein TolC / Macrolide export protein MacA / Macrolide export ATP-binding/permease protein MacB
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria) / Escherichia coli (strain K12) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.3 Å
AuthorsFitzpatrick AWP / Llabres S / Neuberger A / Blaza JN / Bai X-C / Okada U / Murakami S / van Veen HW / Zachariae U / Scheres SHW ...Fitzpatrick AWP / Llabres S / Neuberger A / Blaza JN / Bai X-C / Okada U / Murakami S / van Veen HW / Zachariae U / Scheres SHW / Luisi BF / Du D
Funding support United Kingdom, Japan, 2 items
OrganizationGrant numberCountry
Wellcome TrustRG61065 United Kingdom
Human Frontier Science ProgramRG68784 Japan
CitationJournal: Nat Microbiol / Year: 2017
Title: Structure of the MacAB-TolC ABC-type tripartite multidrug efflux pump.
Authors: Anthony W P Fitzpatrick / Salomé Llabrés / Arthur Neuberger / James N Blaza / Xiao-Chen Bai / Ui Okada / Satoshi Murakami / Hendrik W van Veen / Ulrich Zachariae / Sjors H W Scheres / Ben ...Authors: Anthony W P Fitzpatrick / Salomé Llabrés / Arthur Neuberger / James N Blaza / Xiao-Chen Bai / Ui Okada / Satoshi Murakami / Hendrik W van Veen / Ulrich Zachariae / Sjors H W Scheres / Ben F Luisi / Dijun Du /
Abstract: The MacA-MacB-TolC assembly of Escherichia coli is a transmembrane machine that spans the cell envelope and actively extrudes substrates, including macrolide antibiotics and polypeptide virulence ...The MacA-MacB-TolC assembly of Escherichia coli is a transmembrane machine that spans the cell envelope and actively extrudes substrates, including macrolide antibiotics and polypeptide virulence factors. These transport processes are energized by the ATPase MacB, a member of the ATP-binding cassette (ABC) superfamily. We present an electron cryo-microscopy structure of the ABC-type tripartite assembly at near-atomic resolution. A hexamer of the periplasmic protein MacA bridges between a TolC trimer in the outer membrane and a MacB dimer in the inner membrane, generating a quaternary structure with a central channel for substrate translocation. A gating ring found in MacA is proposed to act as a one-way valve in substrate transport. The MacB structure features an atypical transmembrane domain with a closely packed dimer interface and a periplasmic opening that is the likely portal for substrate entry from the periplasm, with subsequent displacement through an allosteric transport mechanism.
History
DepositionMar 24, 2017-
Header (metadata) releaseMay 24, 2017-
Map releaseMay 24, 2017-
UpdateOct 23, 2019-
Current statusOct 23, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5nil
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3653.png

Downloads & links

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Map

FileDownload / File: emd_3653.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe membrane proximal domain of MacA and MacB
Voxel sizeX=Y=Z: 1.36 Å
Density
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.04176567 - 0.08935645
Average (Standard dev.)0.00019566144 (±0.0024146617)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 408.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.361.361.36
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z408.000408.000408.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0420.0890.000

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Supplemental data

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Sample components

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Entire : MacAB-TolC

EntireName: MacAB-TolC
Components
  • Complex: MacAB-TolC
    • Protein or peptide: Outer membrane protein TolC
    • Protein or peptide: Macrolide export protein MacA
    • Protein or peptide: Macrolide export ATP-binding/permease protein MacB

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Supramolecule #1: MacAB-TolC

SupramoleculeName: MacAB-TolC / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: Outer membrane protein TolC

MacromoleculeName: Outer membrane protein TolC / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria)
Molecular weightTheoretical: 52.506547 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: ENLMQVYQQA RLSNPELRKS AADRDAAFEK INEARSPLLP QLGLGADYTY SNGYRDANGI NSNATSASLQ LTQSIFDMSK WRALTLQEK AAGIQDVTYQ TDQQTLILNT ATAYFNVLNA IDVLSYTQAQ KEAIYRQLDQ TTQRFNVGLV AITDVQNARA Q YDTVLANE ...String:
ENLMQVYQQA RLSNPELRKS AADRDAAFEK INEARSPLLP QLGLGADYTY SNGYRDANGI NSNATSASLQ LTQSIFDMSK WRALTLQEK AAGIQDVTYQ TDQQTLILNT ATAYFNVLNA IDVLSYTQAQ KEAIYRQLDQ TTQRFNVGLV AITDVQNARA Q YDTVLANE LTARNNLDNA VEQLRQITGN YYPELAALNV ENFKTDKPQP VNALLKEAEK RNLSLLQARL SQDLAREQIR QA QDGHLPT LDLTASTGIS DTSYSGSKTR GAAGTQYDDS NMGQNKVGLS FSLPIYQGGM VNSQVKQAQY NFVGASEQLE SAH RSVVQT VRSSFNNINA SISSINAYKQ AVVSAQSSLD AMEAGYSVGT RTIVDVLDAT TTLYNAKQEL ANARYNYLIN QLNI KSALG TLNEQDLLAL NNALSKPVST NPENVAPQTP EQNAIADGYA PDSPAPVVQQ TSARTTTSNG HNPFRNDYKD DDDK

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Macromolecule #2: Macrolide export protein MacA

MacromoleculeName: Macrolide export protein MacA / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria)
Molecular weightTheoretical: 40.715746 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKKRKTVKKR YVIALVIVIA GLITLWRILN APVPTYQTLI VRPGDLQQSV LATGKLDALR KVDVGAQVSG QLKTLSVAIG DKVKKDQLL GVIDPEQAEN QIKEVEATLM ELRAQRQQAE AELKLARVTY SRQQRLAQTQ AVSQQDLDNA ATEMAVKQAQ I GTIDAQIK ...String:
MKKRKTVKKR YVIALVIVIA GLITLWRILN APVPTYQTLI VRPGDLQQSV LATGKLDALR KVDVGAQVSG QLKTLSVAIG DKVKKDQLL GVIDPEQAEN QIKEVEATLM ELRAQRQQAE AELKLARVTY SRQQRLAQTQ AVSQQDLDNA ATEMAVKQAQ I GTIDAQIK RNQASLDTAK TNLDYTRIVA PMAGEVTQIT TLQGQTVIAA QQAPNILTLA DMSAMLVKAQ VSEADVIHLK PG QKAWFTV LGDQLTRYEG QIKDVLPTPE KVNDAIFYYA RFEVPNPNGL LRLDMTAQVH IQLTDVKNVL TIPLSALGDP VGD NRYKVK LLRNGETRER EVTIGARNDT DVEIVKGLEA GDEVVIGEAK PGAAQ

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Macromolecule #3: Macrolide export ATP-binding/permease protein MacB

MacromoleculeName: Macrolide export ATP-binding/permease protein MacB / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances
Source (natural)Organism: Escherichia coli (strain K12) (bacteria)
Molecular weightTheoretical: 71.600094 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTPLLELKDI RRSYPAGDEQ VEVLKGISLD IYAGEMVAIV GASGSGKSTL MNILGCLDKA TSGTYRVAGQ DVATLDADAL AQLRREHFG FIFQRYHLLS HLTAEQNVEV PAVYAGLERK QRLLRAQELL QRLGLEDRTE YYPAQLSGGQ QQRVSIARAL M NGGQVILA ...String:
MTPLLELKDI RRSYPAGDEQ VEVLKGISLD IYAGEMVAIV GASGSGKSTL MNILGCLDKA TSGTYRVAGQ DVATLDADAL AQLRREHFG FIFQRYHLLS HLTAEQNVEV PAVYAGLERK QRLLRAQELL QRLGLEDRTE YYPAQLSGGQ QQRVSIARAL M NGGQVILA DEPTGALDSH SGEEVMAILH QLRDRGHTVI IVTHDPQVAA QAERVIEIRD GEIVRNPPAI EKVNVTGGTE PV VNTVSGW RQFVSGFNEA LTMAWRALAA NKMRTLLTML GIIIGIASVV SIVVVGDAAK QMVLADIRSI GTNTIDVYPG KDF GDDDPQ YQQALKYDDL IAIQKQPWVA SATPAVSQNL RLRYNNVDVA ASANGVSGDY FNVYGMTFSE GNTFNQEQLN GRAQ VVVLD SNTRRQLFPH KADVVGEVIL VGNMPARVIG VAEEKQSMFG SSKVLRVWLP YSTMSGRVMG QSWLNSITVR VKEGF DSAE AEQQLTRLLS LRHGKKDFFT WNMDGVLKTV EKTTRTLQLF LTLVAVISLV VGGIGVMNIM LVSVTERTRE IGIRMA VGA RASDVLQQFL IEAVLVCLVG GALGITLSLL IAFTLQLFLP GWEIGFSPLA LLLAFLCSTV TGILFGWLPA RNAARLD PV DALAREHHHH HH

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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

Concentration2 mg/mL
BufferpH: 8
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: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 2.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 17154

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