+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6zy3 | |||||||||
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タイトル | Cryo-EM structure of MlaFEDB in complex with phospholipid | |||||||||
要素 |
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キーワード | LIPID TRANSPORT / phospholipid / phospholipid transport / ABC transporter / MlaFEDB / MlaFE / MlaD / MlaE / MlaF / MlaB / outer membrane / Mla transport pathway | |||||||||
機能・相同性 | 機能・相同性情報 phospholipid transfer activity / intermembrane phospholipid transfer / phospholipid-translocating ATPase complex / phospholipid transport / ATP-binding cassette (ABC) transporter complex / response to antibiotic / DNA damage response / ATP hydrolysis activity / ATP binding / membrane / cytosol 類似検索 - 分子機能 | |||||||||
生物種 | Escherichia coli B185 (大腸菌) Escherichia coli (大腸菌) Escherichia coli 909945-2 (大腸菌) Escherichia coli 2.3916 (大腸菌) | |||||||||
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: 3.3 Å | |||||||||
データ登録者 | Dong, C.J. / Dong, H.H. | |||||||||
資金援助 | 中国, 英国, 2件
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引用 | ジャーナル: Nat Struct Mol Biol / 年: 2021 タイトル: Structural insights into outer membrane asymmetry maintenance in Gram-negative bacteria by MlaFEDB. 著者: Xiaodi Tang / Shenghai Chang / Wen Qiao / Qinghua Luo / Yuejia Chen / Zhiying Jia / James Coleman / Ke Zhang / Ting Wang / Zhibo Zhang / Changbin Zhang / Xiaofeng Zhu / Xiawei Wei / ...著者: Xiaodi Tang / Shenghai Chang / Wen Qiao / Qinghua Luo / Yuejia Chen / Zhiying Jia / James Coleman / Ke Zhang / Ting Wang / Zhibo Zhang / Changbin Zhang / Xiaofeng Zhu / Xiawei Wei / Changjiang Dong / Xing Zhang / Haohao Dong / 要旨: The highly asymmetric outer membrane of Gram-negative bacteria functions in the defense against cytotoxic substances, such as antibiotics. The Mla pathway maintains outer membrane lipid asymmetry by ...The highly asymmetric outer membrane of Gram-negative bacteria functions in the defense against cytotoxic substances, such as antibiotics. The Mla pathway maintains outer membrane lipid asymmetry by transporting phospholipids between the inner and outer membranes. It comprises six Mla proteins, MlaFEDBCA, including the ABC transporter MlaFEDB, which functions via an unknown mechanism. Here we determine cryo-EM structures of Escherichia coli MlaFEDB in an apo state and bound to phospholipid, ADP or AMP-PNP to a resolution of 3.3-4.1 Å and establish a proteoliposome-based transport system that includes MlaFEDB, MlaC and MlaA-OmpF to monitor the transport direction of phospholipids. In vitro transport assays and in vivo membrane permeability assays combined with mutagenesis identify functional residues that not only recognize and transport phospholipids but also regulate the activity and structural stability of the MlaFEDB complex. Our results provide mechanistic insights into the Mla pathway, which could aid antimicrobial drug development. | |||||||||
履歴 |
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-構造の表示
ムービー |
ムービービューア |
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構造ビューア | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 6zy3.cif.gz | 353.9 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb6zy3.ent.gz | 290 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 6zy3.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
文書・要旨 | 6zy3_validation.pdf.gz | 891.9 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 6zy3_full_validation.pdf.gz | 900.3 KB | 表示 | |
XML形式データ | 6zy3_validation.xml.gz | 54.5 KB | 表示 | |
CIF形式データ | 6zy3_validation.cif.gz | 83.9 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/zy/6zy3 ftp://data.pdbj.org/pub/pdb/validation_reports/zy/6zy3 | HTTPS FTP |
-関連構造データ
-リンク
-集合体
登録構造単位 |
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-要素
#1: タンパク質 | 分子量: 19593.133 Da / 分子数: 6 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli B185 (大腸菌) / 遺伝子: ECDG_03382 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: D6IEA5 #2: タンパク質 | 分子量: 11795.488 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli (大腸菌) 遺伝子: mlaB, yrbB, A6581_13415, A6592_14225, A6V01_00625, A8C65_02170, A9P13_02945, A9R57_12600, A9X72_02835, AC067_23675, ACN002_3282, ACN68_12355, ACN81_18445, ACU57_14445, ACU90_11565, AM270_ ...遺伝子: mlaB, yrbB, A6581_13415, A6592_14225, A6V01_00625, A8C65_02170, A9P13_02945, A9R57_12600, A9X72_02835, AC067_23675, ACN002_3282, ACN68_12355, ACN81_18445, ACU57_14445, ACU90_11565, AM270_15510, AM446_04320, AM464_08585, AMK83_06340, AML07_19340, APT94_23200, APZ14_04295, ARC77_12405, AU473_05735, AUQ13_03075, AUS26_18260, AW106_13275, AWB10_02850, AWG90_020620, AWP75_14100, B9M99_10250, B9T59_16250, BANRA_01811, BANRA_03804, BANRA_03999, BANRA_04207, BB545_09780, BE963_06830, BER14_09135, BHJ80_21985, BHS81_19200, BHS87_17970, BIQ87_18040, BIU72_05405, BJJ90_02770, BK292_10220, BK296_13050, BK373_10175, BK375_18740, BK383_15965, BMA87_01295, BMT49_25595, BMT91_11610, BOH76_04915, BON63_14235, BON66_12205, BON69_26555, BON71_25170, BON72_13935, BON75_23145, BON76_05525, BON83_09240, BON86_01565, BON87_18195, BON92_11035, BON94_12335, BON95_22020, BON96_06355, BTQ04_16475, BTQ06_11870, BUE81_19690, BvCms2454_04822, BvCms28BK_03527, BvCms35BK_01543, BvCmsHHP001_01202, BvCmsHHP019_05314, BvCmsKKP061_00888, BvCmsKSNP073_02163, BvCmsKSNP081_00287, BvCmsKSP011_02050, BvCmsKSP024_00283, BvCmsKSP026_00502, BvCmsKSP045_01650, BvCmsKSP067_01464, BvCmsNSNP036_02151, BvCmsNSP006_04640, BvCmsNSP047_04118, BvCmsNSP072_03187, BvCmsOUP014_03632, BvCmsSINP011_04458, BvCmsSIP019_00407, BvCmsSIP044_00137, BVL39_10130, BW690_19360, BWI89_22070, BWP17_10155, BXT93_02550, BZL31_05925, BZL69_07715, C2M16_04215, C5715_22795, C5N07_18070, C5P01_18835, C6669_12020, C7235_03225, C7B02_15875, C7B08_03565, C7B18_13830, C9098_07790, C9114_15455, C9141_00390, C9160_02340, C9162_04110, C9201_13875, C9306_00415, C9E25_11270, C9E67_03375, C9Z03_07490, C9Z28_00385, C9Z29_07190, C9Z37_14660, C9Z39_14275, C9Z43_00380, C9Z68_06245, C9Z69_11175, C9Z70_06765, C9Z78_03315, C9Z89_09065, CA593_10345, CDL37_12215, CF006_16665, CG692_07300, CI641_009255, CI693_03675, CI694_20835, CIG45_16045, CJU63_19140, CJU64_19020, CMR93_08835, CO706_14630, COD30_12915, COD46_10760, CQP61_03650, CR538_03070, CR539_21250, CRD98_04715, CRE06_06830, CRM83_23500, CRX46_03745, CVH05_10780, CWM24_22870, CWS33_08375, D0X26_09090, D2184_10505, D2185_00445, D2188_02580, D3821_08325, D3822_14575, D3O91_07625, D3P01_09160, D3Y67_18290, D4011_13725, D4074_02435, D4628_02655, D4636_02890, D4638_00790, D4660_02830, D4718_09085, D4L91_11950, D4M06_11225, D4U85_14330, D5H35_09780, D5I97_10670, D6004_08125, D6C36_14160, D6D43_15510, D6T60_15390, D6T98_02410, D6W00_14015, D6X36_05360, D6X63_01430, D6X76_04335, D7K33_12855, D7K63_12220, D7K66_04495, D7W70_15855, D7Z75_02945, D8Y65_13475, D9610_07810, D9C99_05120, D9D20_06275, D9D31_14515, D9D43_03615, D9D44_04410, D9E19_10400, D9E34_11740, D9E49_09595, D9F17_07200, D9F32_01240, D9F87_05870, D9G29_07025, D9G48_11290, D9G69_01100, D9G95_17085, D9H53_01195, D9H68_07560, D9I18_07175, D9I88_07240, D9J03_05150, D9J11_01130, D9J44_07850, D9J52_07915, D9J58_06110, D9J60_11185, D9J63_16910, D9J78_05130, D9K02_06080, D9K48_12255, D9L89_05370, D9S45_00255, D9X77_02330, D9X97_03120, D9Z28_03370, DAH18_20610, DAH26_17315, DAH30_12875, DAH32_13975, DAH34_01980, DAH37_04255, DAH43_16780, DBQ99_04040, DD762_13125, DEN86_08060, DEN89_09405, DEN97_16135, DEO04_19605, DEO19_06430, DIV22_02975, DJ503_19040, DK132_07375, DL257_05650, DL292_05795, DL326_06060, DL455_12700, DL479_06590, DL530_10055, DL705_01300, DL800_23275, DLT82_02655, DLU50_08550, DLU67_08375, DLU82_10330, DLW60_07490, DLW88_04795, DLY41_08155, DM102_15165, DM155_07645, DM267_03265, DM280_09055, DM296_04835, DM382_07360, DM820_04625, DM962_02640, DM973_04650, DMI04_04270, DMI53_12715, DMO02_15405, DMY83_09920, DN660_01330, DN700_04595, DN703_01080, DN808_01890, DNB37_13705, DNC98_07160, DND16_06535, DND79_01330, DNI21_03635, DNJ62_12070, DNK12_02835, DNQ45_01620, DNW42_05405, DNX19_05580, DNX30_11365, DOE35_12610, DOS18_13030, DOT81_04255, DOU81_12375, DOY22_14085, DOY56_12245, DOY61_04695, DOY67_01285, DP265_06555, DP277_10105, DQE83_16545, DQE91_01265, DQF36_08635, DQF57_03615, DQF71_07160, DQF72_06460, DQG35_02830, DQO13_01295, DQP61_01770, DRP48_13910, DRW19_01295, DS143_06770, DS721_11090, DS732_23695, DT034_01270, DTL43_04295, DTM10_06985, DTM45_14510, DTZ20_12090, DU309_11135, DU321_08670, DVB38_07395, DXT69_05520, DXT71_00440, DXX80_009590, E0I42_14340, E0K84_17700, E0L12_03915, E2119_05870, E2127_02575, E2128_02495, E2129_05760, E2134_15595, E2135_08080, E2855_04145, E2863_03970, E4K55_06660, E4K61_09280, E5P22_07075, E5P28_12910, E5P37_13135, E5S42_17100, E5S46_15725, E5S47_16890, E5S58_02935, E5S61_19420, EA214_08600, EA223_04825, EA225_07080, EA233_06175, EAI42_05495, EAI52_09890, EAM59_01020, EAN70_10745, EAX79_13230, EB476_09250, EB509_07200, EB510_12405, EB515_07025, EBA84_05830, EBJ06_06135, EBM08_05455, EC1094V2_454, EC3234A_53c00700, EC3426_04342, EC95NR1_02575, ECTO6_00563, ED225_04270, ED307_11785, ED600_09400, ED607_10425, ED611_04280, ED903_04655, ED944_07260, EEA45_06940, EEP23_06300, EF082_03990, EF173_17005, EG075_10110, EG599_06165, EG796_01190, EG808_04845, EGC26_04915, EGU87_04215, EH186_08760, EH412_00995, EHD45_17860, EHD63_05275, EHD79_13055, EHJ36_00995, EHJ66_06090, EHV81_00555, EHV90_06170, EHW09_05600, EHX09_11795, EI021_04065, EI028_15050, EI032_12380, EI041_02000, EIZ86_06785, EIZ93_11790, EJ366_25995, EJC75_15225, EKI52_18235, EL75_0496, EL79_0518, EL80_0509, ELT20_05045, ELU85_06925, ELV05_02275, ELV08_02985, ELV15_01830, ELV28_06345, EPT01_00415, EQ820_11545, EQ823_05050, EQ830_04520, ERL57_13435, ERS085365_00538, ERS085366_00551, ERS085374_01930, ERS085379_00371, ERS085383_00695, ERS085404_02185, ERS085406_02933, ERS085416_00356, ERS139211_02331, ERS150873_02331, ERS150876_01029, EST51_02745, EVY14_07725, EXM29_19995, ExPECSC019_00712, ExPECSC038_02702, EXX71_13400, EXX78_16730, EYD11_02645, EYX82_02455, EYY34_10615, F1E19_20375, F7F00_12170, F7F11_09035, F7F18_01205, F7F23_11445, F7F26_00405, F7F29_05115, F7G01_13980, F7G03_16150, F9Z74_11630, FAF34_018885, FE846_13735, FKO60_06240, FNJ69_14865, FNJ83_20565, FORC82_0569, FQ022_08190, FQ915_12490, FQR64_03035, FQZ46_16130, FTV92_21230, FV293_08375, FVB16_04440, FWK02_19645, FY127_07380, FZ043_22035, GHR40_07595, GII67_12750, GIY13_09305, GIY19_08335, GJ11_20810, GJD97_02885, GKE15_04665, GKE22_12205, GKE24_04655, GKE26_04130, GKE29_02675, GKE31_04620, GKE39_10535, GKE46_11210, GKE58_04575, GKE60_04100, GKE64_10535, GKE77_05005, GKE87_00910, GKE93_06185, GKF00_03235, GKF03_05520, GKF28_12045, GKF34_04640, GKF47_04635, GKF74_09220, GKF86_04260, GKF89_14375, GKG12_08325, GN312_06640, GNZ00_05080, GNZ02_01290, GNZ03_06110, GP654_17710, GP661_13045, GP664_12080, GP666_12960, GP689_13875, GP712_11385, GP935_13340, GP946_08670, GP950_18225, GQE30_02570, GQE34_13735, GQE51_04670, GQE64_09725, GQE68_06200, GQE88_20265, GQE93_14850, GQM06_05785, GQM09_11065, GQM13_09420, GQM17_12885, GQN16_09500, GRW42_15935, GRW80_12045, HmCmsJML074_04878, HmCmsJML079_04444, HmCmsJML204_02250, HMPREF3040_00351, HW43_20915, MJ49_14345, NCTC10082_02946, NCTC10090_03637, NCTC10418_00837, NCTC10764_03982, NCTC10766_02903, NCTC10865_00786, NCTC10963_00565, NCTC10974_00682, NCTC11022_03358, NCTC11341_01768, NCTC12650_00838, NCTC12950_00597, NCTC13127_00906, NCTC13216_01244, NCTC7922_03906, NCTC7927_00668, NCTC8179_06070, NCTC8500_00486, NCTC8622_00353, NCTC8960_03188, NCTC8985_05122, NCTC9007_04416, NCTC9044_01237, NCTC9050_03718, NCTC9055_02489, NCTC9062_02576, NCTC9077_00732, NCTC9111_00974, NCTC9117_00877, NCTC9701_00685, NCTC9702_00649, NCTC9703_05076, NCTC9706_02844, NCTC9777_02009, PGD_03924, RG28_21075, RK56_014610, RX35_04279, SAMEA3472043_01825, SAMEA3472047_01897, SAMEA3472055_00376, SAMEA3472070_01148, SAMEA3472080_00969, SAMEA3472090_00572, SAMEA3472110_01519, SAMEA3472112_01503, SAMEA3472114_00459, SAMEA3472147_01902, SAMEA3484427_00584, SAMEA3484429_00758, SAMEA3484434_03617, SAMEA3752372_01803, SAMEA3752553_01163, SAMEA3752557_01851, SAMEA3752559_03249, SAMEA3752620_02365, SAMEA3753064_02960, SAMEA3753164_02324, SAMEA3753290_00124, SAMEA3753300_02107, SK85_03504, UC41_09935, UN86_15380, WQ89_06640, WR15_24440, YDC107_1864 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: W8T4U6, UniProt: P64602*PLUS #3: タンパク質 | 分子量: 29128.801 Da / 分子数: 2 / 由来タイプ: 組換発現 由来: (組換発現) Escherichia coli 909945-2 (大腸菌) 遺伝子: HMPREF1620_02486 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: V0AC37 #4: タンパク質 | 分子量: 27885.162 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli 2.3916 (大腸菌) / 遺伝子: EC23916_1052 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: I2X585 #5: 化合物 | ChemComp-PEE / | 研究の焦点であるリガンドがあるか | Y | |
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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 |
-試料調製
構成要素 |
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由来(天然) |
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由来(組換発現) |
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緩衝液 | pH: 7.8 / 詳細: 20 mM Tris-Cl, pH 7.8, 150 mM NaCl and 0.05% LMNG | ||||||||||||||||||||||||||||||||||||
緩衝液成分 |
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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 / 湿度: 95 % / 凍結前の試料温度: 298 K |
-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: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD |
撮影 | 電子線照射量: 40 e/Å2 フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) |
-解析
ソフトウェア | 名称: PHENIX / バージョン: 1.14_3260: / 分類: 精密化 | |||||||||||||||||||||
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EMソフトウェア |
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CTF補正 | タイプ: PHASE FLIPPING ONLY | |||||||||||||||||||||
対称性 | 点対称性: C1 (非対称) | |||||||||||||||||||||
3次元再構成 | 解像度: 3.3 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 97672 / アルゴリズム: FOURIER SPACE / クラス平均像の数: 2 / 対称性のタイプ: POINT | |||||||||||||||||||||
原子モデル構築 | B value: 77 / プロトコル: AB INITIO MODEL / 空間: RECIPROCAL |