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万見- EMDB-22116: Cryo-EM structure of MlaFEDB in nanodiscs with phospholipid substrates -
+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-22116 | |||||||||||||||||||||||||||||||||||||||
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タイトル | Cryo-EM structure of MlaFEDB in nanodiscs with phospholipid substrates | |||||||||||||||||||||||||||||||||||||||
マップデータ | MlaFEDB cryo-em density map, scharpened at -50 A^2 and cropped to 300x300x300 pixels. | |||||||||||||||||||||||||||||||||||||||
試料 |
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キーワード | lipid transport / bacterial cell envelope / mla pathway / MCE | |||||||||||||||||||||||||||||||||||||||
機能・相同性 | 機能・相同性情報 加水分解酵素; 酸無水物に作用; 酸無水物に作用・物質の膜輸送を触媒する / phospholipid transport / ATPase-coupled transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / hydrolase activity / ATP binding 類似検索 - 分子機能 | |||||||||||||||||||||||||||||||||||||||
生物種 | Escherichia coli K-12 (大腸菌) / Escherichia coli DEC6A (大腸菌) / Homo sapiens (ヒト) | |||||||||||||||||||||||||||||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.05 Å | |||||||||||||||||||||||||||||||||||||||
データ登録者 | Coudray N / Isom GL | |||||||||||||||||||||||||||||||||||||||
資金援助 | 米国, 12件
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引用 | ジャーナル: Elife / 年: 2020 タイトル: Structure of bacterial phospholipid transporter MlaFEDB with substrate bound. 著者: Nicolas Coudray / Georgia L Isom / Mark R MacRae / Mariyah N Saiduddin / Gira Bhabha / Damian C Ekiert / 要旨: In double-membraned bacteria, phospholipid transport across the cell envelope is critical to maintain the outer membrane barrier, which plays a key role in virulence and antibiotic resistance. An MCE ...In double-membraned bacteria, phospholipid transport across the cell envelope is critical to maintain the outer membrane barrier, which plays a key role in virulence and antibiotic resistance. An MCE transport system called Mla has been implicated in phospholipid trafficking and outer membrane integrity, and includes an ABC transporter, MlaFEDB. The transmembrane subunit, MlaE, has minimal sequence similarity to other transporters, and the structure of the entire inner-membrane MlaFEDB complex remains unknown. Here, we report the cryo-EM structure of MlaFEDB at 3.05 Å resolution, revealing distant relationships to the LPS and MacAB transporters, as well as the eukaryotic ABCA/ABCG families. A continuous transport pathway extends from the MlaE substrate-binding site, through the channel of MlaD, and into the periplasm. Unexpectedly, two phospholipids are bound to MlaFEDB, suggesting that multiple lipid substrates may be transported each cycle. Our structure provides mechanistic insight into substrate recognition and transport by MlaFEDB. | |||||||||||||||||||||||||||||||||||||||
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 | EMマップ: SurfViewMolmilJmol/JSmol |
添付画像 |
-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_22116.map.gz | 95.6 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-22116-v30.xml emd-22116.xml | 23.8 KB 23.8 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_22116.png | 177.3 KB | ||
Filedesc metadata | emd-22116.cif.gz | 7 KB | ||
その他 | emd_22116_additional.map.gz | 238.3 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-22116 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22116 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_22116_validation.pdf.gz | 553.3 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_22116_full_validation.pdf.gz | 552.9 KB | 表示 | |
XML形式データ | emd_22116_validation.xml.gz | 6.6 KB | 表示 | |
CIF形式データ | emd_22116_validation.cif.gz | 7.5 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22116 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22116 | HTTPS FTP |
-関連構造データ
関連構造データ | 6xbdMC M: このマップから作成された原子モデル C: 同じ文献を引用 (文献) |
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類似構造データ | |
電子顕微鏡画像生データ | EMPIAR-10536 (タイトル: Single particle cryo-EM dataset for MlaFEDB from E. coli in nanodisc Data size: 5.2 TB Data #1: Unaligned multi-frame micrographs of MlaFEDB complex [micrographs - multiframe] Data #2: Polished particles (using Relion 3.1) [picked particles - single frame - processed]) |
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
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「今月の分子」の関連する項目 |
-マップ
ファイル | ダウンロード / ファイル: emd_22116.map.gz / 形式: CCP4 / 大きさ: 103 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | MlaFEDB cryo-em density map, scharpened at -50 A^2 and cropped to 300x300x300 pixels. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 0.832 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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-添付データ
-追加マップ: MlaFEDB cryo-em density map (unsharpened and uncropped)
ファイル | emd_22116_additional.map | ||||||||||||
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注釈 | MlaFEDB cryo-em density map (unsharpened and uncropped) | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-試料の構成要素
-全体 : MlaFEDB complex with two bound phospholipid substrates in MSP1D1 ...
全体 | 名称: MlaFEDB complex with two bound phospholipid substrates in MSP1D1 nanodisc |
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要素 |
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-超分子 #1: MlaFEDB complex with two bound phospholipid substrates in MSP1D1 ...
超分子 | 名称: MlaFEDB complex with two bound phospholipid substrates in MSP1D1 nanodisc タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1-#5 |
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由来(天然) | 生物種: Escherichia coli K-12 (大腸菌) |
分子量 | 理論値: 266 KDa |
-分子 #1: Phospholipid ABC transporter-binding protein MlaD
分子 | 名称: Phospholipid ABC transporter-binding protein MlaD / タイプ: protein_or_peptide / ID: 1 / コピー数: 6 / 光学異性体: LEVO |
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由来(天然) | 生物種: Escherichia coli DEC6A (大腸菌) |
分子量 | 理論値: 21.937674 KDa |
組換発現 | 生物種: Escherichia coli Rosetta 2 (DE3) (大腸菌) |
配列 | 文字列: MHHHHHHQHQ HENLYFQGMQ TKKNEIWVGI FLLAALLAAL FVCLKAANVT SIRTEPTYTL YATFDNIGGL KARSPVSIGG VVVGRVADI TLDPKTYLPR VTLEIEQRYN HIPDTSSLSI RTSGLLGEQY LALNVGFEDP ELGTAILKDG DTIQDTKSAM V LEDLIGQF ...文字列: MHHHHHHQHQ HENLYFQGMQ TKKNEIWVGI FLLAALLAAL FVCLKAANVT SIRTEPTYTL YATFDNIGGL KARSPVSIGG VVVGRVADI TLDPKTYLPR VTLEIEQRYN HIPDTSSLSI RTSGLLGEQY LALNVGFEDP ELGTAILKDG DTIQDTKSAM V LEDLIGQF LYGSKGDDNK NSGDAPAAAP GNNETTEPVG TTK UniProtKB: Putative phospholipid ABC transporter-binding protein mlaD |
-分子 #2: Phospholipid ABC transporter permease protein MlaE
分子 | 名称: Phospholipid ABC transporter permease protein MlaE / タイプ: protein_or_peptide / ID: 2 / コピー数: 2 / 光学異性体: LEVO |
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由来(天然) | 生物種: Escherichia coli DEC6A (大腸菌) |
分子量 | 理論値: 27.885162 KDa |
組換発現 | 生物種: Escherichia coli Rosetta 2 (DE3) (大腸菌) |
配列 | 文字列: MLLNALASLG HKGIKTLRTF GRAGLMLFNA LVGKPEFRKH APLLVRQLYN VGVLSMLIIV VSGVFIGMVL GLQGYLVLTT YSAETSLGM LVALSLLREL GPVVAALLFA GRAGSALTAE IGLMRATEQL SSMEMMAVDP LRRVISPRFW AGVISLPLLT V IFVAVGIW ...文字列: MLLNALASLG HKGIKTLRTF GRAGLMLFNA LVGKPEFRKH APLLVRQLYN VGVLSMLIIV VSGVFIGMVL GLQGYLVLTT YSAETSLGM LVALSLLREL GPVVAALLFA GRAGSALTAE IGLMRATEQL SSMEMMAVDP LRRVISPRFW AGVISLPLLT V IFVAVGIW GGSLVGVSWK GIDSGFFWSA MQNAVDWRMD LVNCLIKSVV FAITVTWISL FNGYDAIPTS AGISRATTRT VV HSSLAVL GLDFVLTALM FGN UniProtKB: Intermembrane phospholipid transport system permease protein MlaE |
-分子 #3: Phospholipid transport system ATP-binding protein MlaF
分子 | 名称: Phospholipid transport system ATP-binding protein MlaF タイプ: protein_or_peptide / ID: 3 / コピー数: 2 / 光学異性体: LEVO EC番号: 加水分解酵素; 酸無水物に作用; 酸無水物に作用・物質の膜輸送を触媒する |
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由来(天然) | 生物種: Escherichia coli DEC6A (大腸菌) |
分子量 | 理論値: 29.128801 KDa |
組換発現 | 生物種: Escherichia coli Rosetta 2 (DE3) (大腸菌) |
配列 | 文字列: MEQSVANLVD MRDVSFTRGN RCIFDNISLT VPRGKITAIM GPSGIGKTTL LRLIGGQIAP DHGEILFDGE NIPAMSRSRL YTVRKRMSM LFQSGALFTD MNVFDNVAYP LREHTQLPAP LLHSTVMMKL EAVGLRGAAK LMPSELSGGM ARRAALARAI A LEPDLIMF ...文字列: MEQSVANLVD MRDVSFTRGN RCIFDNISLT VPRGKITAIM GPSGIGKTTL LRLIGGQIAP DHGEILFDGE NIPAMSRSRL YTVRKRMSM LFQSGALFTD MNVFDNVAYP LREHTQLPAP LLHSTVMMKL EAVGLRGAAK LMPSELSGGM ARRAALARAI A LEPDLIMF DEPFVGQDPI TMGVLVKLIS ELNSALGVTC VVVSHDVPEV LSIADHAWIL ADKKIVAHGS AQALQANPDP RV RQFLDGI ADGPVPFRYP AGDYHADLLP GS UniProtKB: Putative phospholipid import ATP-binding protein MlaF |
-分子 #4: Phospholipid ABC transporter-binding protein MlaB
分子 | 名称: Phospholipid ABC transporter-binding protein MlaB / タイプ: protein_or_peptide / ID: 4 / コピー数: 2 / 光学異性体: LEVO |
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由来(天然) | 生物種: Escherichia coli K-12 (大腸菌) |
分子量 | 理論値: 10.690313 KDa |
組換発現 | 生物種: Escherichia coli Rosetta 2 (DE3) (大腸菌) |
配列 | 文字列: MSESLSWMQT GDTLALSGEL DQDVLLPLWE MREEAVKGIT CIDLSRVSRV DTGGLALLLH LIDLAKKQGN NVTLQGVNDK VYTLAKLYN LPADVLPR UniProtKB: Putative phospholipid ABC transporter-binding protein mlaB |
-分子 #5: MSP1D1
分子 | 名称: MSP1D1 / タイプ: protein_or_peptide / ID: 5 / コピー数: 2 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 13.975214 KDa |
組換発現 | 生物種: Escherichia coli Rosetta 2 (DE3) (大腸菌) |
配列 | 文字列: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) ...文字列: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) |
-分子 #6: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE
分子 | 名称: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / タイプ: ligand / ID: 6 / コピー数: 2 / 式: PEF |
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分子量 | 理論値: 691.959 Da |
Chemical component information | ChemComp-PEF: |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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解析 | 単粒子再構成法 |
試料の集合状態 | particle |
-試料調製
濃度 | 0.95 mg/mL |
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緩衝液 | pH: 7.4 |
グリッド | モデル: Quantifoil R1.2/1.3 / メッシュ: 400 / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: HOLEY / 前処理 - タイプ: GLOW DISCHARGE |
凍結 | 凍結剤: ETHANE / 装置: FEI VITROBOT MARK IV |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 検出モード: SUPER-RESOLUTION / デジタル化 - 画像ごとのフレーム数: 1-30 / 撮影したグリッド数: 1 / 実像数: 3212 / 平均露光時間: 6.0 sec. / 平均電子線量: 71.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm / 倍率(公称値): 29000 |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |