+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6ttu | ||||||
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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 | ||||||
要素 |
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キーワード | LIGASE / Ubiquitin / E3 ligase / NEDD8 / cullin / CUL1 / RBX1 / SKP1 / TRCP / UBE2D / IkBalpha / Neddylation / Ubiquitylation | ||||||
機能・相同性 | 機能・相同性情報 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 / IkBA variant leads to EDA-ID / nucleotide-binding oligomerization domain containing 1 signaling pathway / 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 / IkBA variant leads to EDA-ID / nucleotide-binding oligomerization domain containing 1 signaling pathway / 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 / RIP-mediated NFkB activation via ZBP1 / positive regulation of ubiquitin protein ligase activity / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / ubiquitin ligase activator activity / Cul7-RING ubiquitin ligase complex / SUMOylation of immune response proteins / maintenance of protein location in nucleus / positive regulation of circadian rhythm / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / regulation of proteolysis / nucleotide-binding oligomerization domain containing 2 signaling pathway / positive regulation of protein autoubiquitination / protein neddylation / transcription regulator inhibitor activity / regulation of canonical NF-kappaB signal transduction / branching involved in mammary gland duct morphogenesis / regulation of canonical Wnt signaling pathway / NEDD8 ligase activity / interleukin-1-mediated signaling pathway / Cul5-RING ubiquitin ligase complex / negative regulation of response to oxidative stress / cellular response to cold / non-canonical NF-kappaB signal transduction / mammary gland epithelial cell proliferation / ubiquitin-ubiquitin ligase activity / SCF ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / toll-like receptor 4 signaling pathway / Cul4A-RING E3 ubiquitin ligase complex / negative regulation of NF-kappaB transcription factor activity / negative regulation of type I interferon production / nuclear localization sequence binding / ubiquitin ligase complex scaffold activity / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Cul4B-RING E3 ubiquitin ligase complex / negative regulation of T cell receptor signaling pathway / E2 ubiquitin-conjugating enzyme / Cul3-RING ubiquitin ligase complex / negative regulation of Notch signaling pathway / response to exogenous dsRNA / Prolactin receptor signaling / ligase activity / TGF-beta receptor signaling activates SMADs / protein monoubiquitination / cullin family protein binding / transcription factor binding / ubiquitin conjugating enzyme activity / TRAF6 mediated NF-kB activation / response to muramyl dipeptide / positive regulation of proteolysis / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / cellular response to organic cyclic compound / NF-kappaB binding / ubiquitin-like ligase-substrate adaptor activity / positive regulation of cholesterol efflux / anatomical structure morphogenesis / positive regulation of transcription initiation by RNA polymerase II / protein autoubiquitination / protein K48-linked ubiquitination / canonical NF-kappaB signal transduction / Nuclear events stimulated by ALK signaling in cancer / regulation of proteasomal protein catabolic process / negative regulation of canonical NF-kappaB signal transduction / ubiquitin ligase complex / negative regulation of smoothened signaling pathway / lipopolysaccharide-mediated signaling pathway / Maturation of protein E / Notch signaling pathway / Maturation of protein E / tumor necrosis factor-mediated signaling pathway / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / FLT3 signaling by CBL mutants / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Prevention of phagosomal-lysosomal fusion / Glycogen synthesis / protein sequestering activity / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Endosomal Sorting Complex Required For Transport (ESCRT) / TICAM1,TRAF6-dependent induction of TAK1 complex 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: 3.7 Å | ||||||
データ登録者 | Baek, K. / Prabu, J.R. / Schulman, B.A. | ||||||
資金援助 | ドイツ, 1件
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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 |
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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 | 6ttu.cif.gz | 298 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb6ttu.ent.gz | 239.4 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 6ttu.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 | 6ttu_validation.pdf.gz | 1.1 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 6ttu_full_validation.pdf.gz | 1.1 MB | 表示 | |
XML形式データ | 6ttu_validation.xml.gz | 61.2 KB | 表示 | |
CIF形式データ | 6ttu_validation.cif.gz | 90.9 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/tt/6ttu ftp://data.pdbj.org/pub/pdb/validation_reports/tt/6ttu | 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
-タンパク質 , 7種, 7分子 TSCNRDU
#1: タンパク質 | 分子量: 68960.797 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: BTRC, BTRCP, FBW1A, FBXW1A / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q9Y297 |
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#2: タンパク質 | 分子量: 18679.965 Da / 分子数: 1 / 由来タイプ: 組換発現 / 詳細: SKP1 contains truncations of residues 38-43, 71-82. / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: SKP1, EMC19, OCP2, SKP1A, TCEB1L / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: P63208 |
#3: タンパク質 | 分子量: 89800.367 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CUL1 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q13616 |
#4: タンパク質 | 分子量: 8661.055 Da / 分子数: 1 / 由来タイプ: 組換発現 詳細: Residue 1, Ser, comes from the linker. NEDD8 residue starts from MET. 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: NEDD8 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: Q15843 |
#5: タンパク質 | 分子量: 12333.067 Da / 分子数: 1 / 由来タイプ: 組換発現 詳細: RBX1 contains mutation Asn98Arg (N98R). There are 3 Zinc ions coordinated throughout. This is not meant to align to the C-terminus of the protein. 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: RBX1, RNF75, ROC1 / 発現宿主: Escherichia coli (大腸菌) 参照: UniProt: P62877, UniProt: H2QLR9*PLUS, RING-type E3 ubiquitin transferase, cullin-RING-type E3 NEDD8 transferase |
#6: タンパク質 | 分子量: 16745.121 Da / 分子数: 1 / 由来タイプ: 組換発現 詳細: UBE2D2 contains mutations of the following: Cys21Ile, Cys107Ala, Cys111Asp. 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B / 発現宿主: Escherichia coli (大腸菌) 参照: UniProt: P62837, E2 ubiquitin-conjugating enzyme, (E3-independent) E2 ubiquitin-conjugating enzyme |
#7: タンパク質 | 分子量: 8576.831 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: UBC / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P0CG48 |
-タンパク質・ペプチド / 非ポリマー , 2種, 4分子 I
#8: タンパク質・ペプチド | 分子量: 3782.819 Da / 分子数: 1 / 由来タイプ: 合成 / 詳細: Phosphorylated peptide derived from IkBa. / 由来: (合成) Homo sapiens (ヒト) / 参照: UniProt: P25963*PLUS |
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#9: 化合物 |
-詳細
研究の焦点であるリガンドがあるか | N |
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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 |
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分子量 | 値: 0.210 MDa | ||||||||||||||||||||||||||||||||||||
由来(天然) |
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由来(組換発現) |
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緩衝液 | pH: 7.8 | ||||||||||||||||||||||||||||||||||||
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES | ||||||||||||||||||||||||||||||||||||
急速凍結 | 凍結剤: ETHANE-PROPANE |
-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 |
撮影 | 電子線照射量: 70.2 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) |
-解析
ソフトウェア | 名称: PHENIX / バージョン: 1.15.2_3472: / 分類: 精密化 | ||||||||||||||||||||||||
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EMソフトウェア |
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
対称性 | 点対称性: C1 (非対称) | ||||||||||||||||||||||||
3次元再構成 | 解像度: 3.7 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 106257 / 対称性のタイプ: POINT | ||||||||||||||||||||||||
拘束条件 |
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