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- EMDB-64785: Structure of TolC, YbjP, and AcrABZ complex -

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Basic information

Entry
Database: EMDB / ID: EMD-64785
TitleStructure of TolC, YbjP, and AcrABZ complex
Map data
Sample
  • Complex: TolC-YbjP-AcrABZ complex
    • Protein or peptide: Outer membrane protein TolC
    • Protein or peptide: Uncharacterized lipoprotein YbjP
    • Protein or peptide: Multidrug efflux pump subunit AcrA
    • Protein or peptide: Multidrug efflux pump subunit AcrB
    • Protein or peptide: Multidrug efflux pump accessory protein AcrZ
KeywordsMultidrug efflux pump / TolC / YbjP / AcrA / AcrB / lipoprotein / antibiotic resistance / Gram-negative / PROTEIN TRANSPORT
Function / homology
Function and homology information


MacAB-TolC complex / 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 detoxification by transmembrane export across the plasma membrane ...MacAB-TolC complex / 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 detoxification by transmembrane export across the plasma membrane / xenobiotic transport / bile acid and bile salt transport / porin activity / monoatomic ion channel activity / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / fatty acid transport / cell outer membrane / response to toxic substance / outer membrane-bounded periplasmic space / monoatomic ion transmembrane transport / response to xenobiotic stimulus / response to antibiotic / identical protein binding / membrane / plasma membrane
Similarity search - Function
Domain of unknown function DUF3828 / Protein of unknown function (DUF3828) / : / Multidrug efflux pump accessory protein AcrZ / Multidrug efflux pump-associated protein AcrZ / : / Type I secretion outer membrane protein, TolC / : / Cation efflux system protein CusB, domain 1 / : ...Domain of unknown function DUF3828 / Protein of unknown function (DUF3828) / : / Multidrug efflux pump accessory protein AcrZ / Multidrug efflux pump-associated protein AcrZ / : / Type I secretion outer membrane protein, TolC / : / Cation efflux system protein CusB, domain 1 / : / RND efflux pump, membrane fusion protein / RND efflux pump, membrane fusion protein, barrel-sandwich domain / : / Outer membrane efflux protein / Outer membrane efflux protein / Hydrophobe/amphiphile efflux-1 HAE1 / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / Acriflavin resistance protein / AcrB/AcrD/AcrF family / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Outer membrane protein TolC / Multidrug efflux pump accessory protein AcrZ / Multidrug efflux pump subunit AcrA / Multidrug efflux pump subunit AcrB / Uncharacterized lipoprotein YbjP
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / Escherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.39 Å
AuthorsGe XF / Gu ZW / Wang JW
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32371254 China
National Natural Science Foundation of China (NSFC)32171190 China
CitationJournal: To Be Published
Title: Structural mechanisms of pump assembly and drug transport in the AcrAB-TolC efflux system
Authors: Ge XF / Gu ZW / Wang JW
History
DepositionMay 25, 2025-
Header (metadata) releaseNov 5, 2025-
Map releaseNov 5, 2025-
UpdateNov 5, 2025-
Current statusNov 5, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64785.png

Downloads & links

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Map

FileDownload / File: emd_64785.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 512 pix.
= 691.2 Å		1.35 Å/pix.
x 512 pix.
= 691.2 Å		1.35 Å/pix.
x 512 pix.
= 691.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.29
Minimum - Maximum-0.73024315 - 1.4949237
Average (Standard dev.)-0.00016810244 (±0.04500794)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 691.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_64785_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_64785_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : TolC-YbjP-AcrABZ complex

EntireName: TolC-YbjP-AcrABZ complex
Components
  • Complex: TolC-YbjP-AcrABZ complex
    • Protein or peptide: Outer membrane protein TolC
    • Protein or peptide: Uncharacterized lipoprotein YbjP
    • Protein or peptide: Multidrug efflux pump subunit AcrA
    • Protein or peptide: Multidrug efflux pump subunit AcrB
    • Protein or peptide: Multidrug efflux pump accessory protein AcrZ

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Supramolecule #1: TolC-YbjP-AcrABZ complex

SupramoleculeName: TolC-YbjP-AcrABZ complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: 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 K-12 (bacteria)
Molecular weightTheoretical: 53.783355 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKKLLPILIG LSLSGFSSLS QAENLMQVYQ QARLSNPELR KSAADRDAAF EKINEARSPL LPQLGLGADY TYSNGYRDAN GINSNATSA SLQLTQSIFD MSKWRALTLQ EKAAGIQDVT YQTDQQTLIL NTATAYFNVL NAIDVLSYTQ AQKEAIYRQL D QTTQRFNV ...String:
MKKLLPILIG LSLSGFSSLS QAENLMQVYQ QARLSNPELR KSAADRDAAF EKINEARSPL LPQLGLGADY TYSNGYRDAN GINSNATSA SLQLTQSIFD MSKWRALTLQ EKAAGIQDVT YQTDQQTLIL NTATAYFNVL NAIDVLSYTQ AQKEAIYRQL D QTTQRFNV GLVAITDVQN ARAQYDTVLA NEVTARNNLD NAVEQLRQIT GNYYPELAAL NVENFKTDKP QPVNALLKEA EK RNLSLLQ ARLSQDLARE QIRQAQDGHL PTLDLTASTG ISDTSYSGSK TRGAAGTQYD DSNMGQNKVG LSFSLPIYQG GMV NSQVKQ AQYNFVGASE QLESAHRSVV QTVRSSFNNI NASISSINAY KQAVVSAQSS LDAMEAGYSV GTRTIVDVLD ATTT LYNAK QELANARYNY LINQLNIKSA LGTLNEQDLL ALNNALSKPV STNPENVAPQ TPEQNAIADG YAPDSPAPVV QQTSA RTTT SNGHNPFRN

UniProtKB: Outer membrane protein TolC

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Macromolecule #2: Uncharacterized lipoprotein YbjP

MacromoleculeName: Uncharacterized lipoprotein YbjP / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 19.013287 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MRYSKLTMLI PCALLLSACT TVTPAYKDNG TRSGPCVEGG PDNVAQQFYD YRILHRSNDI TALRPYLSDK LATLLSDASR DNNHRELLT NDPFSSRTTL PDSAHVASAS TIPNRDARNI PLRVDLKQGD QGWQDEVLMI QEGQCWVIDD VRYLGGSVHA T AGTLRQSI ENR

UniProtKB: Uncharacterized lipoprotein YbjP

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Macromolecule #3: Multidrug efflux pump subunit AcrA

MacromoleculeName: Multidrug efflux pump subunit AcrA / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 42.237488 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNKNRGFTPL AVVLMLSGSL ALTGCDDKQA QQGGQQMPAV GVVTVKTEPL QITTELPGRT SAYRIAEVRP QVSGIILKRN FKEGSDIEA GVSLYQIDPA TYQATYDSAK GDLAKAQAAA NIAQLTVNRY QKLLGTQYIS KQEYDQALAD AQQANAAVTA A KAAVETAR ...String:
MNKNRGFTPL AVVLMLSGSL ALTGCDDKQA QQGGQQMPAV GVVTVKTEPL QITTELPGRT SAYRIAEVRP QVSGIILKRN FKEGSDIEA GVSLYQIDPA TYQATYDSAK GDLAKAQAAA NIAQLTVNRY QKLLGTQYIS KQEYDQALAD AQQANAAVTA A KAAVETAR INLAYTKVTS PISGRIGKSN VTEGALVQNG QATALATVQQ LDPIYVDVTQ SSNDFLRLKQ ELANGTLKQE NG KAKVSLI TSDGIKFPQD GTLEFSDVTV DQTTGSITLR AIFPNPDHTL LPGMFVRARL EEGLNPNAIL VPQQGVTRTP RGD ATVLVV GADDKVETRP IVASQAIGDK WLVTEGLKAG DRVVISGLQK VRPGVQVKAQ EVTADNNQQA ASGAQPEQSK S

UniProtKB: Multidrug efflux pump subunit AcrA

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Macromolecule #4: Multidrug efflux pump subunit AcrB

MacromoleculeName: Multidrug efflux pump subunit AcrB / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 113.66518 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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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Macromolecule #5: Multidrug efflux pump accessory protein AcrZ

MacromoleculeName: Multidrug efflux pump accessory protein AcrZ / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 5.304423 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MLELLKSLVF AVIMVPVVMA IILGLIYGLG EVFNIFSGVG KKDQPGQNH

UniProtKB: Multidrug efflux pump accessory protein AcrZ

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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

BufferpH: 8
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeFEI TECNAI F30
Image recordingFilm or detector model: GATAN K3 (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: 1.8 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 31000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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