登録情報 データベース : EMDB / ID : EMD-10585 構造の表示 ダウンロードとリンクタイトル Ubiquitin Ligation to substrate by a cullin-RING E3 ligase at 3.7A resolution: NEDD8-CUL1-RBX1 N98R-SKP1-monomeric b-TRCP1dD-IkBa-UB~UBE2D2 マップデータ 詳細 試料複合体 : Ubiquitin Ligation to substrate by a cullin-RING E3 ligase at 3.7A resolution: NEDD8-CUL1-RBX1 N98R-SKP1-monomeric b-TRCP1dD-IkBa-UB~UBE2D2複合体 : S-phase kinase-associated protein 1タンパク質・ペプチド : E3 ubiquitin-protein ligase RBX1複合体 : Cullin-1, E3 ubiquitin-protein ligase RBX1タンパク質・ペプチド : S-phase kinase-associated protein 1タンパク質・ペプチド : NEDD8複合体 : F-box/WD repeat-containing protein 1A, NEDD8, S-phase kinase-associated protein 1, Ubiquitin-conjugating enzyme E2 D2タンパク質・ペプチド : F-box/WD repeat-containing protein 1Aタンパク質・ペプチド : Cullin-1タンパク質・ペプチド : Ubiquitin-conjugating enzyme E2 D2タンパク質・ペプチド : Polyubiquitin-C複合体 : Synthetic peptide ペプチド合成タンパク質・ペプチド : CYS-LYS-LYS-ALA-ARG-HIS-ASP-SEP-GLYリガンド : ZINC ION 詳細機能・相同性 機能・相同性情報分子機能 ドメイン・相同性 構成要素
I-kappaB/NF-kappaB complex / protein phosphorylated amino acid binding / cytoplasmic sequestering of NF-kappaB / Parkin-FBXW7-Cul1 ubiquitin ligase complex / negative regulation of myeloid cell differentiation / F-box domain binding / nucleotide-binding oligomerization domain containing 1 signaling pathway / IkBA variant leads to EDA-ID / PcG protein complex / (E3-independent) E2 ubiquitin-conjugating enzyme ... I-kappaB/NF-kappaB complex / protein phosphorylated amino acid binding / cytoplasmic sequestering of NF-kappaB / Parkin-FBXW7-Cul1 ubiquitin ligase complex / negative regulation of myeloid cell differentiation / F-box domain binding / nucleotide-binding oligomerization domain containing 1 signaling pathway / IkBA variant leads to EDA-ID / PcG protein complex / (E3-independent) E2 ubiquitin-conjugating enzyme / cullin-RING-type E3 NEDD8 transferase / cellular response to chemical stress / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / molecular sequestering activity / ubiquitin ligase activator activity / Cul7-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / RIP-mediated NFkB activation via ZBP1 / positive regulation of ubiquitin protein ligase activity / SUMOylation of immune response proteins / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / regulation of proteolysis / positive regulation of circadian rhythm / maintenance of protein location in nucleus / nucleotide-binding oligomerization domain containing 2 signaling pathway / positive regulation of protein autoubiquitination / protein neddylation / regulation of canonical Wnt signaling pathway / transcription regulator inhibitor activity / branching involved in mammary gland duct morphogenesis / regulation of canonical NF-kappaB signal transduction / NEDD8 ligase activity / Cul5-RING ubiquitin ligase complex / ubiquitin-ubiquitin ligase activity / interleukin-1-mediated signaling pathway / cellular response to cold / mammary gland epithelial cell proliferation / Cul4A-RING E3 ubiquitin ligase complex / SCF複合体 / Cul2-RING ubiquitin ligase complex / negative regulation of type I interferon production / toll-like receptor 4 signaling pathway / nuclear localization sequence binding / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / ユビキチン結合酵素 / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Cul3-RING ubiquitin ligase complex / negative regulation of NF-kappaB transcription factor activity / negative regulation of Notch signaling pathway / response to exogenous dsRNA / Prolactin receptor signaling / TGF-beta receptor signaling activates SMADs / non-canonical NF-kappaB signal transduction / protein monoubiquitination / ligase activity / ubiquitin conjugating enzyme activity / cullin family protein binding / positive regulation of proteolysis / TRAF6 mediated NF-kB activation / response to muramyl dipeptide / transcription factor binding / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / cellular response to organic cyclic compound / ubiquitin-like ligase-substrate adaptor activity / NF-kappaB binding / positive regulation of transcription initiation by RNA polymerase II / positive regulation of cholesterol efflux / anatomical structure morphogenesis / canonical NF-kappaB signal transduction / Nuclear events stimulated by ALK signaling in cancer / protein autoubiquitination / protein K48-linked ubiquitination / negative regulation of smoothened signaling pathway / regulation of proteasomal protein catabolic process / negative regulation of canonical NF-kappaB signal transduction / ubiquitin ligase complex / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / lipopolysaccharide-mediated signaling pathway / Myoclonic epilepsy of Lafora / Notchシグナリング / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / グリコーゲン合成 / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / positive regulation of TORC1 signaling / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination 類似検索 - 分子機能 D domain of beta-TrCP / D domain of beta-TrCP / D domain of beta-TrCP / Ankyrin repeats (many copies) / Nedd8-like ubiquitin / A Receptor for Ubiquitination Targets / F-box domain profile. / F-box-like domain superfamily / F-box-like / SKP1 component, dimerisation ... D domain of beta-TrCP / D domain of beta-TrCP / D domain of beta-TrCP / Ankyrin repeats (many copies) / Nedd8-like ubiquitin / A Receptor for Ubiquitination Targets / F-box domain profile. / F-box-like domain superfamily / F-box-like / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / Fボックスタンパク質 / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / Cullin protein neddylation domain / Cullin, conserved site / Cullin family signature. / Cullin / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin protein neddylation domain / Cullin / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin family / Cullin family profile. / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / ユビキチン結合酵素 / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / SKP1/BTB/POZ domain superfamily / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Zinc finger RING-type profile. / Zinc finger, RING-type / Ankyrin repeat-containing domain superfamily / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / ユビキチン様タンパク質 / G-protein beta WD-40 repeat / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Winged helix DNA-binding domain superfamily / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40リピート / WD40リピート / WD40-repeat-containing domain superfamily / Winged helix-like DNA-binding domain superfamily / WD40/YVTN repeat-like-containing domain superfamily 類似検索 - ドメイン・相同性 Ring-box 1 / Polyubiquitin-C / NF-kappa-B inhibitor alpha / Ubiquitin-conjugating enzyme E2 D2 / E3 ubiquitin-protein ligase RBX1 / S-phase kinase-associated protein 1 / Cullin-1 / NEDD8 / F-box/WD repeat-containing protein 1A 類似検索 - 構成要素生物種 Pan troglodytes (チンパンジー) / 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 : 3.7 Å 詳細 データ登録者Baek K / Prabu JR / Schulman BA 資金援助 ドイツ, 1件 詳細 詳細を隠すOrganization Grant number 国 Max Planck Society ドイツ
引用ジャーナル : Nature / 年 : 2020タイトル : NEDD8 nucleates a multivalent cullin-RING-UBE2D ubiquitin ligation assembly.著者 : Kheewoong Baek / David T Krist / J Rajan Prabu / Spencer Hill / Maren Klügel / Lisa-Marie Neumaier / Susanne von Gronau / Gary Kleiger / Brenda A Schulman / 要旨 : Eukaryotic cell biology depends on cullin-RING E3 ligase (CRL)-catalysed protein ubiquitylation, which is tightly controlled by the modification of cullin with the ubiquitin-like protein NEDD8. ... Eukaryotic cell biology depends on cullin-RING E3 ligase (CRL)-catalysed protein ubiquitylation, which is tightly controlled by the modification of cullin with the ubiquitin-like protein NEDD8. However, how CRLs catalyse ubiquitylation, and the basis of NEDD8 activation, remain unknown. Here we report the cryo-electron microscopy structure of a chemically trapped complex that represents the ubiquitylation intermediate, in which the neddylated CRL1 promotes the transfer of ubiquitin from the E2 ubiquitin-conjugating enzyme UBE2D to its recruited substrate, phosphorylated IκBα. NEDD8 acts as a nexus that binds disparate cullin elements and the RING-activated ubiquitin-linked UBE2D. Local structural remodelling of NEDD8 and large-scale movements of CRL domains converge to juxtapose the substrate and the ubiquitylation active site. These findings explain how a distinctive ubiquitin-like protein alters the functions of its targets, and show how numerous NEDD8-dependent interprotein interactions and conformational changes synergistically configure a catalytic CRL architecture that is both robust, to enable rapid ubiquitylation of the substrate, and fragile, to enable the subsequent functions of cullin-RING proteins. 履歴 登録 2019年12月30日 - ヘッダ(付随情報) 公開 2020年2月12日 - マップ公開 2020年2月12日 - 更新 2020年12月2日 - 現状 2020年12月2日 処理サイト : PDBe / 状態 : 公開
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