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基本情報
登録情報 | データベース: PDB / ID: 8f56 | ||||||
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タイトル | Dimer of aminoglycoside efflux pump AcrD treated with gentamicin | ||||||
![]() | Efflux pump membrane transporter | ||||||
![]() | MEMBRANE PROTEIN / aminoglycoside efflux pump / AcrD / E.coli | ||||||
機能・相同性 | 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![]() | ||||||
生物種 | ![]() ![]() | ||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 2.98 Å | ||||||
![]() | Zhang, Z. | ||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Cryo-EM Structures of AcrD Illuminate a Mechanism for Capturing Aminoglycosides from Its Central Cavity. 著者: Zhemin Zhang / Christopher E Morgan / Meng Cui / Edward W Yu / ![]() 要旨: 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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構造の表示
構造ビューア | 分子: ![]() ![]() |
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PDBx/mmCIF形式 | ![]() | 341.6 KB | 表示 | ![]() |
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PDB形式 | ![]() | 274.2 KB | 表示 | ![]() |
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その他 | ![]() |
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アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
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-関連構造データ
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リンク
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集合体
登録構造単位 | ![]()
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要素
#1: タンパク質 | 分子量: 113139.891 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() 遺伝子: 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_ ...遺伝子: 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 発現宿主: ![]() ![]() |
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-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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EM実験 | 試料の集合状態: PARTICLE / 3次元再構成法: 単粒子再構成法 |
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試料調製
構成要素 | 名称: AcrD / タイプ: COMPLEX / Entity ID: all / 由来: RECOMBINANT |
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由来(天然) | 生物種: ![]() ![]() |
由来(組換発現) | 生物種: ![]() ![]() |
緩衝液 | pH: 7.5 |
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
急速凍結 | 凍結剤: ETHANE |
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電子顕微鏡撮影
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TITAN KRIOS |
電子銃 | 電子線源: ![]() |
電子レンズ | モード: BRIGHT FIELD / 倍率(公称値): 81000 X / 最大 デフォーカス(公称値): 1500 nm / 最小 デフォーカス(公称値): 800 nm |
撮影 | 電子線照射量: 35.7 e/Å2 フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) |
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解析
ソフトウェア | 名称: PHENIX / バージョン: 1.20.1_4487: / 分類: 精密化 | ||||||||||||||||||||||||
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3次元再構成 | 解像度: 2.98 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 53193 / 対称性のタイプ: POINT | ||||||||||||||||||||||||
拘束条件 |
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