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Open data
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Basic information
Entry | Database: PDB / ID: 8f56 | ||||||
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Title | Dimer of aminoglycoside efflux pump AcrD treated with gentamicin | ||||||
![]() | Efflux pump membrane transporter | ||||||
![]() | MEMBRANE PROTEIN / aminoglycoside efflux pump / AcrD / E.coli | ||||||
Function / homology | Hydrophobe/amphiphile efflux-1 HAE1 / Acriflavin resistance protein / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / AcrB/AcrD/AcrF family / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / plasma membrane / Efflux pump membrane transporter![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.98 Å | ||||||
![]() | Zhang, Z. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM Structures of AcrD Illuminate a Mechanism for Capturing Aminoglycosides from Its Central Cavity. Authors: Zhemin Zhang / Christopher E Morgan / Meng Cui / Edward W Yu / ![]() Abstract: The Escherichia coli acriflavine resistance protein D (AcrD) is an efflux pump that belongs to the resistance-nodulation-cell division (RND) superfamily. Its primary function is to provide resistance ...The Escherichia coli acriflavine resistance protein D (AcrD) is an efflux pump that belongs to the resistance-nodulation-cell division (RND) superfamily. Its primary function is to provide resistance to aminoglycoside-based drugs by actively extruding these noxious compounds out of E. coli cells. AcrD can also mediate resistance to a limited range of other amphiphilic agents, including bile acids, novobiocin, and fusidic acids. As there is no structural information available for any aminoglycoside-specific RND pump, here we describe cryo-electron microscopy (cryo-EM) structures of AcrD in the absence and presence of bound gentamicin. These structures provide new information about the RND superfamily of efflux pumps, specifically, that three negatively charged residues central to the aminoglycoside-binding site are located within the ceiling of the central cavity of the AcrD trimer. Thus, it is likely that AcrD is capable of picking up aminoglycosides via this central cavity. Through the combination of cryo-EM structural determination, mutagenesis analysis, and molecular simulation, we show that charged residues are critically important for this pump to shuttle drugs directly from the central cavity to the funnel of the AcrD trimer for extrusion. Here, we report cryo-EM structures of the AcrD aminoglycoside efflux pump in the absence and presence of bound gentamicin, posing the possibility that this pump is capable of capturing aminoglycosides from the central cavity of the AcrD trimer. The results indicate that AcrD utilizes charged residues to bind and export drugs, mediating resistance to these antibiotics. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 341.6 KB | Display | ![]() |
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PDB format | ![]() | 274.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 28861MC ![]() 8f3eC ![]() 8f4nC ![]() 8f4rC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 113139.891 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: acrD, ACU57_04565, BANRA_03325, BJI68_01485, BJJ90_06945, BMT91_11990, BON93_11695, BUO55_002264, C0P57_000121, C5N07_10560, C5Y87_22760, C9160_05345, CTR35_000190, CX938_001812, D3Y67_13030, ...Gene: acrD, ACU57_04565, BANRA_03325, BJI68_01485, BJJ90_06945, BMT91_11990, BON93_11695, BUO55_002264, C0P57_000121, C5N07_10560, C5Y87_22760, C9160_05345, CTR35_000190, CX938_001812, D3Y67_13030, DAH22_02795, DAH27_02260, DAH28_02170, DAH32_09030, DAH37_20010, DAH41_00685, DAH50_04680, DIV22_31685, E2119_05090, E2122_05015, E2127_22975, E2128_11985, E2132_10115, E2134_09425, E4T14_01660, E5P26_05645, E5P27_06290, E5P28_04085, E5P29_08410, E5P31_03360, E5P32_02065, E5P40_06505, E5P51_11900, E5S36_11905, E5S45_03290, EC1094V2_1219, ECs3332, ED648_19550, EI021_07760, EIZ93_19695, EKI52_22415, EL79_1194, EL80_1199, ELT21_03480, ERS139208_00580, EYV17_00615, EYV18_00295, F2N20_03885, F2N31_04825, F9V24_02735, FFF58_09795, FOI11_000625, FOI11_19425, FQF29_08200, G3V95_05155, G4A38_06285, G4A47_09235, GJO56_19765, GKF89_16975, GOP25_13330, GP975_00825, GRW05_00965, HMV95_10675, HNC36_05080, HX136_06730, IH772_01085, J0541_000250, JNP96_20105, NCTC8960_04125, NCTC9037_01546, SAMEA3472044_02066, SAMEA3753106_01071 Production host: ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: AcrD / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 35.7 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 53193 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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