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Yorodumi- EMDB-3636: multi-drug efflux; membrane transport; RND superfamily; Drug resi... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3636 | |||||||||
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Title | multi-drug efflux; membrane transport; RND superfamily; Drug resistance | |||||||||
Map data | AcrABZ-TolC pump with inhibitor MBX3132 bound AcrB in the TTT state | |||||||||
Sample |
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Function / homology | Function and homology information MacAB-TolC complex / alkane transmembrane transporter activity / alkane transport / xenobiotic detoxification by transmembrane export across the cell outer membrane / efflux pump complex / enterobactin transport / enterobactin transmembrane transporter activity / periplasmic side of plasma membrane / bile acid transmembrane transporter activity / xenobiotic detoxification by transmembrane export across the plasma membrane ...MacAB-TolC complex / alkane transmembrane transporter activity / alkane transport / xenobiotic detoxification by transmembrane export across the cell outer membrane / efflux pump complex / enterobactin transport / enterobactin transmembrane transporter activity / periplasmic side of plasma membrane / bile acid transmembrane transporter activity / xenobiotic detoxification by transmembrane export across the plasma membrane / bile acid and bile salt transport / xenobiotic transport / porin activity / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / transmembrane transporter activity / fatty acid transport / monoatomic ion channel activity / cell outer membrane / response to organic cyclic compound / response to toxic substance / monoatomic ion transmembrane transport / outer membrane-bounded periplasmic space / response to xenobiotic stimulus / response to antibiotic / identical protein binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.5 Å | |||||||||
Authors | Wang Z / Fan G / Hryc CF / Blaza JN / Serysheva II / Schmid MF / Chiu W / Luisi BF / Du D | |||||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_3636.map.gz | 105.2 MB | EMDB map data format | |
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Header (meta data) | emd-3636-v30.xml emd-3636.xml | 17.7 KB 17.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_3636_fsc.xml | 10.9 KB | Display | FSC data file |
Images | emd_3636.png | 78.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3636 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3636 | HTTPS FTP |
-Validation report
Summary document | emd_3636_validation.pdf.gz | 321.7 KB | Display | EMDB validaton report |
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Full document | emd_3636_full_validation.pdf.gz | 320.8 KB | Display | |
Data in XML | emd_3636_validation.xml.gz | 11.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3636 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3636 | HTTPS FTP |
-Related structure data
Related structure data | 5ng5MC 8636C 8640C 5nc5C 5o66C 5v5sC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_3636.map.gz / Format: CCP4 / Size: 113.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | AcrABZ-TolC pump with inhibitor MBX3132 bound AcrB in the TTT state | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.29 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : AcrABTolC in apo state
Entire | Name: AcrABTolC in apo state |
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Components |
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-Supramolecule #1: AcrABTolC in apo state
Supramolecule | Name: AcrABTolC in apo state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: Multidrug efflux pump subunit AcrA
Macromolecule | Name: Multidrug efflux pump subunit AcrA / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 39.80066 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: 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
Macromolecule | Name: Outer membrane protein TolC / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 53.783355 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: 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
Macromolecule | Name: Multidrug efflux pump subunit AcrB / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 113.66518 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: 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
Macromolecule | Name: Multidrug efflux pump accessory protein AcrZ / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 5.995157 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MLELLKSLVF AVIMVPVVMA IILGLIYGLG EVFNIFSGVG KKDQPGQNHH HHHH |
-Macromolecule #5: 6-[2-(3,4-dimethoxyphenyl)ethylsulfanyl]-8-[4-(2-methoxyethyl)pip...
Macromolecule | Name: 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 |
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Molecular weight | Theoretical: 526.691 Da |
Chemical component information | ChemComp-5QF: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL |
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Buffer | pH: 8 |
Grid | Model: Quantifoil / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 20 K / Instrument: FEI VITROBOT MARK IV Details: a 3ul aliquot at a concentration of 2 mg per ml was applied onto glow-discharged holey carbon grid (Quantifoil Au R1.21.3, 300 mesh). |
Details | AcrABTolC complex in apo state |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Details | Crystal structures were rigid-body fit into the density map and model optimization was then carried out with Phenix real-space refine. Due to the weaker resolution, stronger stereochemical and secondary structure restraints were used to ensure that alpha-helices and beta-sheets did not deviate far from their expected geometry. Manual adjustments were kept to a minimum to reduce human bias in the modeling procedure, with Coot only being used to fix obvious errors such as C-beta deviations. A final check of MolProbity and cross correlation was done to ensure model quality. |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Target criteria: Cross-correlation coefficient |
Output model | PDB-5ng5: |