+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-10100 | ||||||||||||
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タイトル | Legionella pneumophila SidJ-Human calmodulin complex | ||||||||||||
マップデータ | SidJ_Cam map | ||||||||||||
試料 |
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キーワード | Bacterial glutamylase / pseudo kinase / calmodulin-dependent / Legionella / SidJ / SdeA / serine ubiquitination / transferase | ||||||||||||
機能・相同性 | 機能・相同性情報 合成酵素 / negative regulation of calcium ion transmembrane transporter activity / positive regulation of cyclic-nucleotide phosphodiesterase activity / negative regulation of calcium ion export across plasma membrane / positive regulation of ryanodine-sensitive calcium-release channel activity / regulation of cell communication by electrical coupling involved in cardiac conduction / negative regulation of peptidyl-threonine phosphorylation / protein phosphatase activator activity / ligase activity / positive regulation of phosphoprotein phosphatase activity ...合成酵素 / negative regulation of calcium ion transmembrane transporter activity / positive regulation of cyclic-nucleotide phosphodiesterase activity / negative regulation of calcium ion export across plasma membrane / positive regulation of ryanodine-sensitive calcium-release channel activity / regulation of cell communication by electrical coupling involved in cardiac conduction / negative regulation of peptidyl-threonine phosphorylation / protein phosphatase activator activity / ligase activity / positive regulation of phosphoprotein phosphatase activity / adenylate cyclase binding / catalytic complex / detection of calcium ion / regulation of cardiac muscle contraction / negative regulation of ryanodine-sensitive calcium-release channel activity / calcium channel inhibitor activity / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / cysteine-type peptidase activity / positive regulation of protein dephosphorylation / regulation of calcium-mediated signaling / titin binding / positive regulation of protein autophosphorylation / voltage-gated potassium channel complex / sperm midpiece / calcium channel complex / substantia nigra development / adenylate cyclase activator activity / regulation of heart rate / sarcomere / protein serine/threonine kinase activator activity / positive regulation of peptidyl-threonine phosphorylation / regulation of cytokinesis / positive regulation of protein serine/threonine kinase activity / spindle microtubule / spindle pole / response to calcium ion / G2/M transition of mitotic cell cycle / calcium-dependent protein binding / myelin sheath / transferase activity / vesicle / transmembrane transporter binding / G protein-coupled receptor signaling pathway / nucleotide binding / centrosome / calcium ion binding / protein kinase binding / protein-containing complex / proteolysis / membrane / nucleus / metal ion binding / plasma membrane / cytoplasm 類似検索 - 分子機能 | ||||||||||||
生物種 | Legionella pneumophila (バクテリア) / 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: 4.15 Å | ||||||||||||
データ登録者 | Pfleiderer MM / Galej WP / Adams M / Bhogaraju S | ||||||||||||
資金援助 | ドイツ, 3件
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引用 | ジャーナル: Nature / 年: 2019 タイトル: Inhibition of bacterial ubiquitin ligases by SidJ-calmodulin catalysed glutamylation. 著者: Sagar Bhogaraju / Florian Bonn / Rukmini Mukherjee / Michael Adams / Moritz M Pfleiderer / Wojciech P Galej / Vigor Matkovic / Jaime Lopez-Mosqueda / Sissy Kalayil / Donghyuk Shin / Ivan Dikic / 要旨: The family of bacterial SidE enzymes catalyses phosphoribosyl-linked serine ubiquitination and promotes infectivity of Legionella pneumophila, a pathogenic bacteria that causes Legionnaires' disease. ...The family of bacterial SidE enzymes catalyses phosphoribosyl-linked serine ubiquitination and promotes infectivity of Legionella pneumophila, a pathogenic bacteria that causes Legionnaires' disease. SidE enzymes share the genetic locus with the Legionella effector SidJ that spatiotemporally opposes the toxicity of these enzymes in yeast and mammalian cells, through a mechanism that is currently unknown. Deletion of SidJ leads to a substantial defect in the growth of Legionella in both its natural hosts (amoebae) and in mouse macrophages. Here we demonstrate that SidJ is a glutamylase that modifies the catalytic glutamate in the mono-ADP ribosyl transferase domain of the SdeA, thus blocking the ubiquitin ligase activity of SdeA. The glutamylation activity of SidJ requires interaction with the eukaryotic-specific co-factor calmodulin, and can be regulated by intracellular changes in Ca concentrations. The cryo-electron microscopy structure of SidJ in complex with human apo-calmodulin revealed the architecture of this heterodimeric glutamylase. We show that, in cells infected with L. pneumophila, SidJ mediates the glutamylation of SidE enzymes on the surface of vacuoles that contain Legionella. We used quantitative proteomics to uncover multiple host proteins as putative targets of SidJ-mediated glutamylation. Our study reveals the mechanism by which SidE ligases are inhibited by a SidJ-calmodulin glutamylase, and opens avenues for exploring an understudied protein modification (glutamylation) in eukaryotes. | ||||||||||||
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_10100.map.gz | 11.9 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-10100-v30.xml emd-10100.xml | 18.1 KB 18.1 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_10100_fsc.xml | 5.8 KB | 表示 | FSCデータファイル |
画像 | emd_10100.png | 28.3 KB | ||
Filedesc metadata | emd-10100.cif.gz | 6.1 KB | ||
その他 | emd_10100_half_map_1.map.gz emd_10100_half_map_2.map.gz | 11.9 MB 11.9 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-10100 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10100 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_10100_validation.pdf.gz | 773.9 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_10100_full_validation.pdf.gz | 773.5 KB | 表示 | |
XML形式データ | emd_10100_validation.xml.gz | 11.3 KB | 表示 | |
CIF形式データ | emd_10100_validation.cif.gz | 15.4 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10100 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10100 | HTTPS FTP |
-関連構造データ
-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_10100.map.gz / 形式: CCP4 / 大きさ: 15.6 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | SidJ_Cam map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 0.96 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
-ハーフマップ: #2
ファイル | emd_10100_half_map_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #1
ファイル | emd_10100_half_map_2.map | ||||||||||||
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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 : Legionella pneumophila SidJ - human calmodulin complex
全体 | 名称: Legionella pneumophila SidJ - human calmodulin complex |
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要素 |
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-超分子 #1: Legionella pneumophila SidJ - human calmodulin complex
超分子 | 名称: Legionella pneumophila SidJ - human calmodulin complex タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1-#2 |
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分子量 | 理論値: 120 KDa |
-超分子 #2: SidJ
超分子 | 名称: SidJ / タイプ: complex / ID: 2 / 親要素: 1 / 含まれる分子: #1 |
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由来(天然) | 生物種: Legionella pneumophila (バクテリア) |
-超分子 #3: calmodulin
超分子 | 名称: calmodulin / タイプ: complex / ID: 3 / 親要素: 1 / 含まれる分子: #2 |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
-分子 #1: SidJ
分子 | 名称: SidJ / タイプ: protein_or_peptide / ID: 1 / コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: Legionella pneumophila (バクテリア) |
分子量 | 理論値: 100.338469 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) |
配列 | 文字列: MFGFIKKVLD FFGVDQSEDN PSETAVETTD VSTKIKTTDT TQEESSVKTK TVVPTQPGGS VKPETIAPDQ QKKHQIKTET TTSTTKQKG PKVTLMDGHV KQYYFARRGE TSTHDTSLPP PVKVLSGRSI PLKEIPFEAT RNELVQIYLT SIDKLIKSNK L NSIPSQQI ...文字列: MFGFIKKVLD FFGVDQSEDN PSETAVETTD VSTKIKTTDT TQEESSVKTK TVVPTQPGGS VKPETIAPDQ QKKHQIKTET TTSTTKQKG PKVTLMDGHV KQYYFARRGE TSTHDTSLPP PVKVLSGRSI PLKEIPFEAT RNELVQIYLT SIDKLIKSNK L NSIPSQQI ASHYLFLRSL ANSETDGIKK NQILSLAKPL GTYLASKEPH VWKMINELIE KSEYPIIHYL KNNRAHSNFM LA LIHEYHK EPLTKNQSAF VQKFRDSSVF LFPNPIYTAW LAHSYDEDSS FNPMFRERLS TNFYHSTLTD NLLLRTEPKE VTL SSEHHY KKEKGPIDSS FRYQMSSDRL LRIQGRTLLF STPQNDVVAV KVQKKGEPKS TLEEEFEMAD YLLKHQRRLD VHSK LPQPL GQYSVKKSEI LEISRGSLDF ERFKTLIDDS KDLEVYVYKA PQSYFTYLHD KNQDLEDLTA SVKTNVHDLF VLLRE GIVF PQLADIFHTH FGEDEREDKG RYQALVQLLN VLQFQLGRID KWQKAVEYVN LRSSGLADLG DSLPITSLFT SSDFTK HYF SELLTGGYHP TFFDKSSGTA NSLFTGKRRL FGNYLYLNTI AEYLLVIQLT LGSYGDKVTR DMMDKPKKEA VWRELAN VM FTSCAEAIHI MTGIPQSRAL TLLKQRANIE KHFRQTQFWM TPDYSKLDED TLQMEQYSIY SGEPEYEFTD KLVSGVGL S VDGVHQDLGG YNRESPLREL EKLLYATVTL IEGTMQLDKE FFKQLEQVEK ILSGEIKTDA NSCFEAVAQL LDLARPGCH FQKRLVLSYY EEAKLKYPSA PTDAYDSRFQ VVARTNAAIT IQRFWREARK NLSEKSDIDS EKPESERTTD KRL UniProtKB: Calmodulin-dependent glutamylase SidJ |
-分子 #2: Calmodulin-2
分子 | 名称: Calmodulin-2 / タイプ: protein_or_peptide / ID: 2 / コピー数: 1 / 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: 16.852545 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) |
配列 | 文字列: MADQLTEEQI AEFKEAFSLF DKDGDGTITT KELGTVMRSL GQNPTEAELQ DMINEVDADG NGTIDFPEFL TMMARKMKDT DSEEEIREA FRVFDKDGNG YISAAELRHV MTNLGEKLTD EEVDEMIREA DIDGDGQVNY EEFVQMMTAK UniProtKB: Calmodulin-2 |
-分子 #3: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
分子 | 名称: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / タイプ: ligand / ID: 3 / コピー数: 1 / 式: ANP |
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分子量 | 理論値: 506.196 Da |
Chemical component information | ChemComp-ANP: |
-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
緩衝液 | pH: 7.5 |
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凍結 | 凍結剤: ETHANE |
詳細 | Recombinant Legionella pneumophila SidJ -human calmodulin complex |
-電子顕微鏡法
顕微鏡 | FEI TALOS ARCTICA |
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撮影 | フィルム・検出器のモデル: FEI FALCON III (4k x 4k) 検出モード: COUNTING / 平均電子線量: 40.0 e/Å2 |
電子線 | 加速電圧: 200 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | C2レンズ絞り径: 70.0 µm / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm |
実験機器 | モデル: Talos Arctica / 画像提供: FEI Company |