+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-8438 | |||||||||||||||
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タイトル | CryoEM reconstruction of human IKK1, closed conformation 3 | |||||||||||||||
マップデータ | CryoEM reconstruction of human IKK1, closed conformation 3, final map | |||||||||||||||
試料 |
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キーワード | kinase / conserved helix-loop-helix / transcription / oncogene / TRANSFERASE | |||||||||||||||
機能・相同性 | 機能・相同性情報 response to acetate / IkappaB kinase / IkappaB kinase activity / IKBKB deficiency causes SCID / IKBKG deficiency causes anhidrotic ectodermal dysplasia with immunodeficiency (EDA-ID) (via TLR) / response to cholecystokinin / IkappaB kinase complex / I-kappaB phosphorylation / transferrin receptor binding / IkBA variant leads to EDA-ID ...response to acetate / IkappaB kinase / IkappaB kinase activity / IKBKB deficiency causes SCID / IKBKG deficiency causes anhidrotic ectodermal dysplasia with immunodeficiency (EDA-ID) (via TLR) / response to cholecystokinin / IkappaB kinase complex / I-kappaB phosphorylation / transferrin receptor binding / IkBA variant leads to EDA-ID / CD40 receptor complex / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / RIP-mediated NFkB activation via ZBP1 / AKT phosphorylates targets in the cytosol / response to hydroperoxide / non-canonical NF-kappaB signal transduction / toll-like receptor 4 signaling pathway / negative regulation of NF-kappaB transcription factor activity / Constitutive Signaling by AKT1 E17K in Cancer / positive regulation of interferon-alpha production / TRAF6 mediated NF-kB activation / Rho protein signal transduction / skeletal muscle contraction / anatomical structure morphogenesis / response to amino acid / canonical NF-kappaB signal transduction / tumor necrosis factor-mediated signaling pathway / striated muscle cell differentiation / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / cellular response to cadmium ion / TICAM1, RIP1-mediated IKK complex recruitment / MAP3K8 (TPL2)-dependent MAPK1/3 activation / IKK complex recruitment mediated by RIP1 / TNFR1-induced NF-kappa-B signaling pathway / Regulation of NF-kappa B signaling / NIK-->noncanonical NF-kB signaling / Dectin-1 mediated noncanonical NF-kB signaling / Activation of NF-kappaB in B cells / Regulation of TNFR1 signaling / NOD1/2 Signaling Pathway / TAK1-dependent IKK and NF-kappa-B activation / response to virus / PKR-mediated signaling / cellular response to virus / CLEC7A (Dectin-1) signaling / response to toxic substance / cytoplasmic side of plasma membrane / FCERI mediated NF-kB activation / Interleukin-1 signaling / cellular response to reactive oxygen species / Downstream TCR signaling / cellular response to tumor necrosis factor / positive regulation of NF-kappaB transcription factor activity / ER-Phagosome pathway / scaffold protein binding / positive regulation of canonical NF-kappaB signal transduction / response to lipopolysaccharide / protein kinase activity / inflammatory response / immune response / response to xenobiotic stimulus / protein heterodimerization activity / protein phosphorylation / innate immune response / protein serine/threonine kinase activity / protein-containing complex binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / positive regulation of DNA-templated transcription / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / cytosol / cytoplasm 類似検索 - 分子機能 | |||||||||||||||
生物種 | 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: 5.2 Å | |||||||||||||||
データ登録者 | Lyumkis D / Ghosh G | |||||||||||||||
資金援助 | 米国, 4件
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引用 | ジャーナル: Cell Rep / 年: 2016 タイトル: Structural Basis for the Activation of IKK1/α. 著者: Smarajit Polley / Dario Oliveira Passos / De-Bin Huang / Maria Carmen Mulero / Anup Mazumder / Tapan Biswas / Inder M Verma / Dmitry Lyumkis / Gourisankar Ghosh / 要旨: Distinct signaling pathways activate the NF-κB family of transcription factors. The canonical NF-κB-signaling pathway is mediated by IκB kinase 2/β (IKK2/β), while the non-canonical pathway ...Distinct signaling pathways activate the NF-κB family of transcription factors. The canonical NF-κB-signaling pathway is mediated by IκB kinase 2/β (IKK2/β), while the non-canonical pathway depends on IKK1/α. The structural and biochemical bases for distinct signaling by these otherwise highly similar IKKs are unclear. We report single-particle cryoelectron microscopy (cryo-EM) and X-ray crystal structures of human IKK1 in dimeric (∼150 kDa) and hexameric (∼450 kDa) forms. The hexamer, which is the representative form in the crystal but comprises only ∼2% of the particles in solution by cryo-EM, is a trimer of IKK1 dimers. While IKK1 hexamers are not detectable in cells, the surface that supports hexamer formation is critical for IKK1-dependent cellular processing of p100 to p52, the hallmark of non-canonical NF-κB signaling. Comparison of this surface to that in IKK2 indicates significant divergence, and it suggests a fundamental role for this surface in signaling by these kinases through distinct pathways. | |||||||||||||||
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_8438.map.gz | 24.8 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-8438-v30.xml emd-8438.xml | 22.4 KB 22.4 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_8438_fsc.xml | 6.8 KB | 表示 | FSCデータファイル |
画像 | emd_8438.png | 149.1 KB | ||
Filedesc metadata | emd-8438.cif.gz | 7.2 KB | ||
その他 | emd_8438_half_map_1.map.gz emd_8438_half_map_2.map.gz | 5.6 MB 5.6 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-8438 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8438 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_8438_validation.pdf.gz | 795.5 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_8438_full_validation.pdf.gz | 795.1 KB | 表示 | |
XML形式データ | emd_8438_validation.xml.gz | 11.4 KB | 表示 | |
CIF形式データ | emd_8438_validation.cif.gz | 16.6 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8438 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8438 | 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_8438.map.gz / 形式: CCP4 / 大きさ: 27 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | CryoEM reconstruction of human IKK1, closed conformation 3, final map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.31 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: CryoEM reconstruction of human IKK1, closed conformation 3,...
ファイル | emd_8438_half_map_1.map | ||||||||||||
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注釈 | CryoEM reconstruction of human IKK1, closed conformation 3, half map 1 | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: CryoEM reconstruction of human IKK1, closed conformation 3,...
ファイル | emd_8438_half_map_2.map | ||||||||||||
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注釈 | CryoEM reconstruction of human IKK1, closed conformation 3, half map 2 | ||||||||||||
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 : Inhibitor of KappaB Kinase 1 dimer
全体 | 名称: Inhibitor of KappaB Kinase 1 dimer |
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要素 |
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-超分子 #1: Inhibitor of KappaB Kinase 1 dimer
超分子 | 名称: Inhibitor of KappaB Kinase 1 dimer / タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: all / 詳細: dimer |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 150 KDa |
-分子 #1: Inhibitor of nuclear factor kappa-B kinase subunit alpha
分子 | 名称: Inhibitor of nuclear factor kappa-B kinase subunit alpha タイプ: protein_or_peptide / ID: 1 / コピー数: 2 / 光学異性体: LEVO / EC番号: IkappaB kinase |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 75.146945 KDa |
組換発現 | 生物種: Spodoptera frugiperda (ツマジロクサヨトウ) |
配列 | 文字列: DPEFGAGGPW EMRERLGTGG FGNVCLYQHR ELDLKIAIKS CRLELSTKNR ERWCHEIQIM KKLNHANVVK ACDVPEELNI LIHDVPLLA MEYCSGGDLR KLLNKPENCC GLKESQILSL LSDIGSGIRY LHENKIIHRD LKPENIVLQD VGGKIIHKII D LGYAKDVD ...文字列: DPEFGAGGPW EMRERLGTGG FGNVCLYQHR ELDLKIAIKS CRLELSTKNR ERWCHEIQIM KKLNHANVVK ACDVPEELNI LIHDVPLLA MEYCSGGDLR KLLNKPENCC GLKESQILSL LSDIGSGIRY LHENKIIHRD LKPENIVLQD VGGKIIHKII D LGYAKDVD QGELCTEFVG TLQYLAPELF ENKPYTATVD YWSFGTMVFE CIAGYRPFLH HLQPFTWHEK IKKKDPKCIF AC EEMSGEV RFSSHLPQPN SLCSLIVEPM ENWLQLMLNW DPQQRGGPVD LTLKQPRCFV LMDHILNLKI VHILNMTSAK IIS FLLPPD ESLHSLQSRI ERETGINTGS QELLSETGIS LDPRKPASQC VLDGVRGCDS YMVYLFDKSK TVYEGPFASR SLSD CVNYI VQDSKIQLPI IQLRKVWAEA VHYVSGLKED YSRLFQGQRA AMLSLLRYNA NLTKMKNTLI SASQQLKAKL EFFHK SIQL DLERYSEQMT YGISSEKMLK AWKEMEEKAI HYAEVGVIGY LEDQIMSLHA EIMELQKSPY GRRQGDLMES LEQRAI DLY KQLKHRPSDH SYSDSTEMVK IIVHTVQSQD RVLKELFGHL SKLLGCKQKI IDLLPKVEVA LSNIKEADNT VMFMQGK RQ KEIWHLLKIA CTQ UniProtKB: Inhibitor of nuclear factor kappa-B kinase subunit alpha |
-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 | 2.5 mg/mL | |||||||||||||||
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緩衝液 | pH: 7.5 構成要素:
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グリッド | モデル: C-flat-1.2/1.3 / 材質: COPPER / 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: PLASMA CLEANING / 前処理 - 時間: 6 sec. / 前処理 - 雰囲気: AIR | |||||||||||||||
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 80 % / チャンバー内温度: 277 K / 装置: HOMEMADE PLUNGER 詳細: Sample containing IKK1 dimers in SEC buffer was applied onto freshly plasma-treated (6 seconds, Gatan Solarus plasma cleaner) holey carbon C-flat grids (Protochips), adsorbed for 30 seconds, ...詳細: Sample containing IKK1 dimers in SEC buffer was applied onto freshly plasma-treated (6 seconds, Gatan Solarus plasma cleaner) holey carbon C-flat grids (Protochips), adsorbed for 30 seconds, and then plunged into liquid ethane using a manual cryo-plunger in an ambient environment of 4 degrees C.. |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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温度 | 最低: 70.0 K / 最高: 70.0 K |
撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 検出モード: COUNTING / デジタル化 - サイズ - 横: 3838 pixel / デジタル化 - サイズ - 縦: 3710 pixel / デジタル化 - 画像ごとのフレーム数: 1-50 / 撮影したグリッド数: 1 / 実像数: 2918 / 平均露光時間: 10.0 sec. / 平均電子線量: 40.0 e/Å2 詳細: The dose was fractionated over 50 raw frames collected over a 10 second exposure time (200 ms per frame) on the Gatan K2 Summit direct detection device, with each frame receiving a dose of ~6. ...詳細: The dose was fractionated over 50 raw frames collected over a 10 second exposure time (200 ms per frame) on the Gatan K2 Summit direct detection device, with each frame receiving a dose of ~6.5 e-/pixel/sec. 2918 movies were collected and recorded at a nominal magnification of 22,500, corresponding to a pixel size of 1.31 A at the specimen level. The individual frames were gain-corrected, then aligned and summed using a GPU-enabled whole frame alignment program (Li et al., 2013), and exposure-filtered (Grant and Grigorieff, 2015). |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | C2レンズ絞り径: 100.0 µm / 最大 デフォーカス(補正後): 5.2 µm / 最小 デフォーカス(補正後): 1.1 µm / 倍率(補正後): 38167 / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm / 倍率(公称値): 22500 |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER ホルダー冷却材: NITROGEN |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
+画像解析
-原子モデル構築 1
精密化 | 空間: REAL / プロトコル: FLEXIBLE FIT / 温度因子: 340 / 当てはまり具合の基準: FSC 0.5 |
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得られたモデル | PDB-5tqy: |