+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 5tqy | |||||||||||||||
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タイトル | CryoEM reconstruction of human IKK1, closed conformation 3 | |||||||||||||||
要素 | Inhibitor of nuclear factor kappa-B kinase subunit alpha | |||||||||||||||
キーワード | TRANSFERASE / kinase / conserved helix-loop-helix / transcription / oncogene | |||||||||||||||
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 / response to hydroperoxide / AKT phosphorylates targets in the cytosol / 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 / TRAF6 mediated NF-kB activation / positive regulation of interferon-alpha production / Rho protein signal transduction / skeletal muscle contraction / cellular response to cadmium ion / anatomical structure morphogenesis / response to amino acid / canonical NF-kappaB signal transduction / striated muscle cell differentiation / tumor necrosis factor-mediated signaling pathway / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / TNFR1-induced NF-kappa-B signaling pathway / NIK-->noncanonical NF-kB signaling / Regulation of NF-kappa B signaling / Dectin-1 mediated noncanonical NF-kB signaling / Activation of NF-kappaB in B cells / Regulation of TNFR1 signaling / cellular response to reactive oxygen species / TAK1-dependent IKK and NF-kappa-B activation / NOD1/2 Signaling Pathway / response to virus / PKR-mediated signaling / cytoplasmic side of plasma membrane / response to toxic substance / cellular response to virus / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / Interleukin-1 signaling / Downstream TCR signaling / cellular response to tumor necrosis factor / positive regulation of NF-kappaB transcription factor activity / positive regulation of canonical NF-kappaB signal transduction / ER-Phagosome pathway / scaffold protein binding / response to lipopolysaccharide / protein kinase activity / response to xenobiotic stimulus / inflammatory response / immune response / protein heterodimerization activity / protein phosphorylation / innate immune response / protein serine/threonine kinase activity / positive regulation of DNA-templated transcription / protein-containing complex binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / nucleoplasm / ATP binding / cytoplasm / cytosol 類似検索 - 分子機能 | |||||||||||||||
生物種 | Homo sapiens (ヒト) | |||||||||||||||
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: 5.2 Å | |||||||||||||||
データ登録者 | Lyumkis, D. / Ghosh, G. / Polley, S. / Biswath, T. / Huang, D. / Passos, D.O. | |||||||||||||||
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 | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 5tqy.cif.gz | 215.7 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb5tqy.ent.gz | 172.3 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 5tqy.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 | 5tqy_validation.pdf.gz | 1.1 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 5tqy_full_validation.pdf.gz | 1.1 MB | 表示 | |
XML形式データ | 5tqy_validation.xml.gz | 40.6 KB | 表示 | |
CIF形式データ | 5tqy_validation.cif.gz | 62.7 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/tq/5tqy ftp://data.pdbj.org/pub/pdb/validation_reports/tq/5tqy | 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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1 |
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-要素
#1: タンパク質 | 分子量: 75146.945 Da / 分子数: 2 / 変異: S176E, S180E / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CHUK, IKKA, TCF16 / プラスミド: pFastBacHTa 発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ) 株 (発現宿主): SF9 / 参照: UniProt: O15111, IkappaB kinase |
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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 | 名称: Inhibitor of KappaB Kinase 1 dimer / タイプ: COMPLEX / 詳細: dimer / Entity ID: all / 由来: RECOMBINANT | |||||||||||||||||||||||||
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分子量 | 値: 0.15 MDa / 実験値: YES | |||||||||||||||||||||||||
由来(天然) | 生物種: Homo sapiens (ヒト) | |||||||||||||||||||||||||
由来(組換発現) | 生物種: Spodoptera frugiperda (ツマジロクサヨトウ) 細胞: SF9 / プラスミド: pFastBacHTa | |||||||||||||||||||||||||
緩衝液 | pH: 7.5 | |||||||||||||||||||||||||
緩衝液成分 |
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試料 | 濃度: 2.5 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES | |||||||||||||||||||||||||
試料支持 | グリッドの材料: COPPER / グリッドのサイズ: 400 divisions/in. / グリッドのタイプ: C-flat-1.2/1.3 | |||||||||||||||||||||||||
急速凍結 | 装置: HOMEMADE PLUNGER / 凍結剤: ETHANE / 湿度: 80 % / 凍結前の試料温度: 277 K 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 / 倍率(公称値): 22500 X / 倍率(補正後): 38167 X / Calibrated defocus min: 1100 nm / 最大 デフォーカス(補正後): 5200 nm / Cs: 2.7 mm / C2レンズ絞り径: 100 µm / アライメント法: COMA FREE |
試料ホルダ | 凍結剤: NITROGEN 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER 最高温度: 70 K / 最低温度: 70 K |
撮影 | 平均露光時間: 10 sec. / 電子線照射量: 40 e/Å2 / 検出モード: COUNTING フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 撮影したグリッド数: 1 / 実像数: 2918 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). |
画像スキャン | サンプリングサイズ: 5 µm / 横: 3838 / 縦: 3710 / 動画フレーム数/画像: 50 / 利用したフレーム数/画像: 1-50 |
-解析
ソフトウェア | 名称: PHENIX / バージョン: dev_2499: / 分類: 精密化 | ||||||||||||||||||||||||||||||||||||||||||||||||||
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EMソフトウェア |
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CTF補正 | 詳細: within Relion and Frealign / タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||
粒子像の選択 | 選択した粒子像数: 230242 | ||||||||||||||||||||||||||||||||||||||||||||||||||
対称性 | 点対称性: C2 (2回回転対称) | ||||||||||||||||||||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 5.2 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 23505 / アルゴリズム: FOURIER SPACE / 対称性のタイプ: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | B value: 340 / プロトコル: FLEXIBLE FIT / 空間: REAL / Target criteria: FSC 0.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 |
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