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Yorodumi- EMDB-10182: Cryo-EM structure of Escherichia coli AcrBZ and DARPin in Saposin... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10182 | |||||||||
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Title | Cryo-EM structure of Escherichia coli AcrBZ and DARPin in Saposin A-nanodisc with cardiolipin | |||||||||
Map data | ||||||||||
Sample |
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Keywords | RND transporter / efflux pump / drug transport / antibiotic resistance / lipid nanodisc / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information 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 / cellular response to cell envelope stress / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / cell outer membrane / membrane => GO:0016020 / response to antibiotic ...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 / cellular response to cell envelope stress / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / cell outer membrane / membrane => GO:0016020 / response to antibiotic / identical protein binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Escherichia coli K-12 (bacteria) / synthetic construct (others) / Shigella boydii 965-58 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.17 Å | |||||||||
Authors | Szewczak-Harris A / Du D | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: Structure / Year: 2020 Title: Interactions of a Bacterial RND Transporter with a Transmembrane Small Protein in a Lipid Environment. Authors: Dijun Du / Arthur Neuberger / Mona Wu Orr / Catherine E Newman / Pin-Chia Hsu / Firdaus Samsudin / Andrzej Szewczak-Harris / Leana M Ramos / Mekdes Debela / Syma Khalid / Gisela Storz / Ben F Luisi / Abstract: The small protein AcrZ in Escherichia coli interacts with the transmembrane portion of the multidrug efflux pump AcrB and increases resistance of the bacterium to a subset of the antibiotic ...The small protein AcrZ in Escherichia coli interacts with the transmembrane portion of the multidrug efflux pump AcrB and increases resistance of the bacterium to a subset of the antibiotic substrates of that transporter. It is not clear how the physical association of the two proteins selectively changes activity of the pump for defined substrates. Here, we report cryo-EM structures of AcrB and the AcrBZ complex in lipid environments, and comparisons suggest that conformational changes occur in the drug-binding pocket as a result of AcrZ binding. Simulations indicate that cardiolipin preferentially interacts with the AcrBZ complex, due to increased contact surface, and we observe that chloramphenicol sensitivity of bacteria lacking AcrZ is exacerbated when combined with cardiolipin deficiency. Taken together, the data suggest that AcrZ and lipid cooperate to allosterically modulate AcrB activity. This mode of regulation by a small protein and lipid may occur for other membrane proteins. | |||||||||
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_10182.map.gz | 96.6 MB | EMDB map data format | |
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Header (meta data) | emd-10182-v30.xml emd-10182.xml | 21.5 KB 21.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10182_fsc.xml | 10.7 KB | Display | FSC data file |
Images | emd_10182.png | 52.5 KB | ||
Masks | emd_10182_msk_1.map | 103 MB | Mask map | |
Filedesc metadata | emd-10182.cif.gz | 6.7 KB | ||
Others | emd_10182_half_map_1.map.gz emd_10182_half_map_2.map.gz | 80.8 MB 80.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10182 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10182 | HTTPS FTP |
-Validation report
Summary document | emd_10182_validation.pdf.gz | 994.2 KB | Display | EMDB validaton report |
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Full document | emd_10182_full_validation.pdf.gz | 993.7 KB | Display | |
Data in XML | emd_10182_validation.xml.gz | 17.7 KB | Display | |
Data in CIF | emd_10182_validation.cif.gz | 23.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10182 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10182 | HTTPS FTP |
-Related structure data
Related structure data | 6sgrMC 6sgsC 6sgtC 6sguC 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_10182.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.088 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_10182_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: None
File | emd_10182_half_map_1.map | ||||||||||||
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Annotation | None | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: None
File | emd_10182_half_map_2.map | ||||||||||||
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Annotation | None | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Ternary complex of AcrBZ and DARPin in Saposin A-nanodisc with ca...
Entire | Name: Ternary complex of AcrBZ and DARPin in Saposin A-nanodisc with cardiolipin |
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Components |
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-Supramolecule #1: Ternary complex of AcrBZ and DARPin in Saposin A-nanodisc with ca...
Supramolecule | Name: Ternary complex of AcrBZ and DARPin in Saposin A-nanodisc with cardiolipin type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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-Supramolecule #2: Multidrug efflux pump subunit AcrB
Supramolecule | Name: Multidrug efflux pump subunit AcrB / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Escherichia coli K-12 (bacteria) |
-Supramolecule #3: DARPin
Supramolecule | Name: DARPin / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: synthetic construct (others) |
-Supramolecule #4: Multidrug efflux pump accessory protein AcrZ
Supramolecule | Name: Multidrug efflux pump accessory protein AcrZ / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3 |
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Source (natural) | Organism: Shigella boydii 965-58 (bacteria) |
-Macromolecule #1: Multidrug efflux pump subunit AcrB
Macromolecule | Name: Multidrug efflux pump subunit AcrB / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli K-12 (bacteria) |
Molecular weight | Theoretical: 113.66518 KDa |
Recombinant expression | Organism: Escherichia coli str. K-12 substr. MG1655 (bacteria) |
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 UniProtKB: Multidrug efflux pump subunit AcrB |
-Macromolecule #2: DARPin
Macromolecule | Name: DARPin / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 18.317566 KDa |
Recombinant expression | Organism: Escherichia coli str. K-12 substr. MG1655 (bacteria) |
Sequence | String: MRGSHHHHHH GSDLGKKLLE AARAGRDDEV RILMANGADV NAADVVGWTP LHLAAYWGHL EIVEVLLKNG ADVNAYDTLG STPLHLAAH FGHLEIVEVL LKNGADVNAK DDNGITPLHL AANRGHLEIV EVLLKYGADV NAQDKFGKTA FDISINNGNE D LAEILQKL N |
-Macromolecule #3: Multidrug efflux pump accessory protein AcrZ
Macromolecule | Name: Multidrug efflux pump accessory protein AcrZ / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli K-12 (bacteria) |
Molecular weight | Theoretical: 5.304423 KDa |
Recombinant expression | Organism: Escherichia coli str. K-12 substr. MG1655 (bacteria) |
Sequence | String: MLELLKSLVF AVIMVPVVMA IILGLIYGLG EVFNIFSGVG KKDQPGQNH UniProtKB: Multidrug efflux pump accessory protein AcrZ |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2.0 mg/mL | |||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.0038 kPa | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV | |||||||||
Details | Monodisperse |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 2720 / Average exposure time: 60.0 sec. / Average electron dose: 46.9 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.4 µm / Nominal defocus min: 1.3 µm / Nominal magnification: 75000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |