[English] 日本語
Yorodumi
- EMDB-8640: Asymmetric structure of AcrAB-TolC tripartite multi drug efflux pump -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-8640
TitleAsymmetric structure of AcrAB-TolC tripartite multi drug efflux pump
Map dataAcrABZ-TolC with puromycin
Sample
  • Complex: AcrABZ-TolC
    • Protein or peptide: Multidrug efflux pump subunit AcrA
    • Protein or peptide: Outer membrane protein TolC
    • Protein or peptide: Multidrug efflux pump subunit AcrB
    • Protein or peptide: Multidrug efflux pump accessory protein AcrZ
  • Ligand: 6-[2-(3,4-dimethoxyphenyl)ethylsulfanyl]-8-[4-(2-methoxyethyl)piperazin-1-yl]-3,3-dimethyl-1,4-dihydropyrano[3,4-c]pyridine-5-carbonitrile
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 / porin activity / xenobiotic transmembrane 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 / porin activity / xenobiotic transmembrane transporter activity / efflux transmembrane transporter activity / transmembrane transporter activity / monoatomic ion transmembrane transport / cell outer membrane / response to organic cyclic compound / response to toxic substance / outer membrane-bounded periplasmic space / monoatomic ion channel activity / response to xenobiotic stimulus / response to antibiotic / membrane / identical protein binding / plasma membrane
Similarity search - Function
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 / Cation efflux system protein CusB domain 1 / RND efflux pump, membrane fusion protein / RND efflux pump, membrane fusion protein, barrel-sandwich domain / Barrel-sandwich domain of CusB or HlyD membrane-fusion / Outer membrane efflux protein / Outer membrane efflux protein ...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 / Cation efflux system protein CusB domain 1 / RND efflux pump, membrane fusion protein / RND efflux pump, membrane fusion protein, barrel-sandwich domain / Barrel-sandwich domain of CusB or HlyD membrane-fusion / Outer membrane efflux protein / Outer membrane efflux protein / Hydrophobe/amphiphile efflux-1 HAE1 / Acriflavin resistance protein / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / 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
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria) / Escherichia coli (strain K12) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.9 Å
AuthorsWang Z / Fan G / Hryc CF / Blaza JN / Serysheva II / Schmid MF / Chiu W / Luisi BF / Du D
CitationJournal: Elife / Year: 2017
Title: An allosteric transport mechanism for the AcrAB-TolC multidrug efflux pump.
Authors: Zhao Wang / Guizhen Fan / Corey F Hryc / James N Blaza / Irina I Serysheva / Michael F Schmid / Wah Chiu / Ben F Luisi / Dijun Du /
Abstract: Bacterial efflux pumps confer multidrug resistance by transporting diverse antibiotics from the cell. In Gram-negative bacteria, some of these pumps form multi-protein assemblies that span the cell ...Bacterial efflux pumps confer multidrug resistance by transporting diverse antibiotics from the cell. In Gram-negative bacteria, some of these pumps form multi-protein assemblies that span the cell envelope. Here, we report the near-atomic resolution cryoEM structures of the AcrAB-TolC multidrug efflux pump in resting and drug transport states, revealing a quaternary structural switch that allosterically couples and synchronizes initial ligand binding with channel opening. Within the transport-activated state, the channel remains open even though the pump cycles through three distinct conformations. Collectively, our data provide a dynamic mechanism for the assembly and operation of the AcrAB-TolC pump.
History
DepositionMar 18, 2017-
Header (metadata) releaseApr 26, 2017-
Map releaseApr 26, 2017-
UpdateJun 14, 2017-
Current statusJun 14, 2017Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5o66
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8640.png

Downloads & links

-
Map

FileDownload / File: emd_8640.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAcrABZ-TolC with puromycin
Voxel sizeX=Y=Z: 1.62 Å
Density
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.08393142 - 0.1429779
Average (Standard dev.)0.000037077272 (±0.011091232)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 414.72 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.621.621.62
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z414.720414.720414.720
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0840.1430.000

-
Supplemental data

-
Sample components

-
Entire : AcrABZ-TolC

EntireName: AcrABZ-TolC
Components
  • Complex: AcrABZ-TolC
    • Protein or peptide: Multidrug efflux pump subunit AcrA
    • Protein or peptide: Outer membrane protein TolC
    • Protein or peptide: Multidrug efflux pump subunit AcrB
    • Protein or peptide: Multidrug efflux pump accessory protein AcrZ
  • Ligand: 6-[2-(3,4-dimethoxyphenyl)ethylsulfanyl]-8-[4-(2-methoxyethyl)piperazin-1-yl]-3,3-dimethyl-1,4-dihydropyrano[3,4-c]pyridine-5-carbonitrile

-
Supramolecule #1: AcrABZ-TolC

SupramoleculeName: AcrABZ-TolC / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Escherichia coli K12 (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)

-
Macromolecule #1: Multidrug efflux pump subunit AcrA

MacromoleculeName: Multidrug efflux pump subunit AcrA / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria)
Molecular weightTheoretical: 39.80066 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: CDDKQAQQGG QQMPAVGVVT VKTEPLQITT ELPGRTSAYR IAEVRPQVSG IILKRNFKEG SDIEAGVSLY QIDPATYQAT YDSAKGDLA KAQAAANIAQ LTVNRYQKLL GTQYISKQEY DQALADAQQA NAAVTAAKAA VETARINLAY TKVTSPISGR I GKSNVTEG ...String:
CDDKQAQQGG QQMPAVGVVT VKTEPLQITT ELPGRTSAYR IAEVRPQVSG IILKRNFKEG SDIEAGVSLY QIDPATYQAT YDSAKGDLA KAQAAANIAQ LTVNRYQKLL GTQYISKQEY DQALADAQQA NAAVTAAKAA VETARINLAY TKVTSPISGR I GKSNVTEG ALVQNGQATA LATVQQLDPI YVDVTQSSND MMRLKQELAN GTLKQENGKA KVSLITSDGI KFPQDGTLEF SD VTVDQTT GSITLRAIFP NPDHTMMPGM FVRARLEEGL NPNAILVPQQ GVTRTPRGDA TVLVVGADDK VETRPIVASQ AIG DKWLVT EGLKAGDRVV ISGLQKVRPG VQVKAQEVTA DNNQQAASGA QPEQSKS

-
Macromolecule #2: Outer membrane protein TolC

MacromoleculeName: Outer membrane protein TolC / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
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

-
Macromolecule #3: Multidrug efflux pump subunit AcrB

MacromoleculeName: Multidrug efflux pump subunit AcrB / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
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

-
Macromolecule #4: Multidrug efflux pump accessory protein AcrZ

MacromoleculeName: Multidrug efflux pump accessory protein AcrZ / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria)
Molecular weightTheoretical: 5.995157 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MLELLKSLVF AVIMVPVVMA IILGLIYGLG EVFNIFSGVG KKDQPGQNHH HHHH

-
Macromolecule #5: 6-[2-(3,4-dimethoxyphenyl)ethylsulfanyl]-8-[4-(2-methoxyethyl)pip...

MacromoleculeName: 6-[2-(3,4-dimethoxyphenyl)ethylsulfanyl]-8-[4-(2-methoxyethyl)piperazin-1-yl]-3,3-dimethyl-1,4-dihydropyrano[3,4-c]pyridine-5-carbonitrile
type: ligand / ID: 5 / Number of copies: 3 / Formula: 5QF
Molecular weightTheoretical: 526.691 Da
Chemical component information

ChemComp-5QF:
6-[2-(3,4-dimethoxyphenyl)ethylsulfanyl]-8-[4-(2-methoxyethyl)piperazin-1-yl]-3,3-dimethyl-1,4-dihydropyrano[3,4-c]pyridine-5-carbonitrile

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI POLARA 300
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) / Detector mode: SUPER-RESOLUTION / Average electron dose: 22.0 e/Å2
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

5915

Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 20349
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more