+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 7b5m | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
タイトル | Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: CUL1-RBX1-SKP1-SKP2-CKSHS1-p27~Ub~ARIH1. Transition State 2 | |||||||||
要素 |
| |||||||||
キーワード | LIGASE / ubiquitin / ubiquitin ligase / E3 ligase / F-box protein / RBR ligase / Cullin-RING-Ligase / CRL / SCF / NEDD8 / Post-translational modification / ubiquitylation | |||||||||
機能・相同性 | 機能・相同性情報 PKR/eIFalpha signaling / cyclin-dependent protein kinase activating kinase regulator activity / regulation of lens fiber cell differentiation / negative regulation of cardiac muscle tissue regeneration / negative regulation of cyclin-dependent protein kinase activity / positive regulation of protein polyubiquitination / ubiquitin-like protein transferase activity / autophagic cell death / Lewy body / Parkin-FBXW7-Cul1 ubiquitin ligase complex ...PKR/eIFalpha signaling / cyclin-dependent protein kinase activating kinase regulator activity / regulation of lens fiber cell differentiation / negative regulation of cardiac muscle tissue regeneration / negative regulation of cyclin-dependent protein kinase activity / positive regulation of protein polyubiquitination / ubiquitin-like protein transferase activity / autophagic cell death / Lewy body / Parkin-FBXW7-Cul1 ubiquitin ligase complex / FOXO-mediated transcription of cell cycle genes / negative regulation of epithelial cell proliferation involved in prostate gland development / F-box domain binding / RBR-type E3 ubiquitin transferase / Aberrant regulation of mitotic exit in cancer due to RB1 defects / PcG protein complex / regulation of cell cycle G1/S phase transition / negative regulation of phosphorylation / regulation of exit from mitosis / cullin-RING-type E3 NEDD8 transferase / mitotic cell cycle phase transition / cellular response to chemical stress / NEDD8 transferase activity / epithelial cell proliferation involved in prostate gland development / cullin-RING ubiquitin ligase complex / negative regulation of epithelial cell apoptotic process / negative regulation of cyclin-dependent protein serine/threonine kinase activity / 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 / maintenance of protein location in nucleus / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / cyclin-dependent protein serine/threonine kinase inhibitor activity / positive regulation of protein autoubiquitination / RHO GTPases activate CIT / protein neddylation / ubiquitin conjugating enzyme binding / cyclin-dependent protein serine/threonine kinase activator activity / nuclear export / NEDD8 ligase activity / Cul5-RING ubiquitin ligase complex / negative regulation of response to oxidative stress / AKT phosphorylates targets in the cytosol / positive regulation of intracellular estrogen receptor signaling pathway / ubiquitin-ubiquitin ligase activity / epithelial cell apoptotic process / SCF ubiquitin ligase complex / cellular response to antibiotic / Cul2-RING ubiquitin ligase complex / Cul4A-RING E3 ubiquitin ligase complex / negative regulation of type I interferon production / ubiquitin ligase complex scaffold activity / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Cul4B-RING E3 ubiquitin ligase complex / Cul3-RING ubiquitin ligase complex / molecular function inhibitor activity / negative regulation of kinase activity / regulation of cyclin-dependent protein serine/threonine kinase activity / cellular response to lithium ion / RSV-host interactions / p53-Dependent G1 DNA Damage Response / protein kinase inhibitor activity / Prolactin receptor signaling / PTK6 Regulates Cell Cycle / regulation of G1/S transition of mitotic cell cycle / protein monoubiquitination / Constitutive Signaling by AKT1 E17K in Cancer / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / negative regulation of vascular associated smooth muscle cell proliferation / cullin family protein binding / inner ear development / protein K63-linked ubiquitination / cellular response to organic cyclic compound / negative regulation of mitotic cell cycle / positive regulation of double-strand break repair via homologous recombination / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / ubiquitin-like ligase-substrate adaptor activity / response to amino acid / protein K48-linked ubiquitination / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / response to cadmium ion / response to glucose / Cajal body / Nuclear events stimulated by ALK signaling in cancer / Cyclin E associated events during G1/S transition / cyclin-dependent protein kinase holoenzyme complex / Cyclin A:Cdk2-associated events at S phase entry / ubiquitin ligase complex / Maturation of protein E / Notch signaling pathway / Maturation of protein E / ER Quality Control Compartment (ERQC) / regulation of mitotic cell cycle / Myoclonic epilepsy of Lafora / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / FLT3 signaling by CBL mutants / positive regulation of microtubule polymerization / IRAK1 recruits IKK 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: 3.91 Å | |||||||||
データ登録者 | Horn-Ghetko, D. / Prabu, J.R. / Schulman, B.A. | |||||||||
資金援助 | ドイツ, 2件
| |||||||||
引用 | ジャーナル: Nature / 年: 2021 タイトル: Ubiquitin ligation to F-box protein targets by SCF-RBR E3-E3 super-assembly. 著者: Daniel Horn-Ghetko / David T Krist / J Rajan Prabu / Kheewoong Baek / Monique P C Mulder / Maren Klügel / Daniel C Scott / Huib Ovaa / Gary Kleiger / Brenda A Schulman / 要旨: E3 ligases are typically classified by hallmark domains such as RING and RBR, which are thought to specify unique catalytic mechanisms of ubiquitin transfer to recruited substrates. However, rather ...E3 ligases are typically classified by hallmark domains such as RING and RBR, which are thought to specify unique catalytic mechanisms of ubiquitin transfer to recruited substrates. However, rather than functioning individually, many neddylated cullin-RING E3 ligases (CRLs) and RBR-type E3 ligases in the ARIH family-which together account for nearly half of all ubiquitin ligases in humans-form E3-E3 super-assemblies. Here, by studying CRLs in the SKP1-CUL1-F-box (SCF) family, we show how neddylated SCF ligases and ARIH1 (an RBR-type E3 ligase) co-evolved to ubiquitylate diverse substrates presented on various F-box proteins. We developed activity-based chemical probes that enabled cryo-electron microscopy visualization of steps in E3-E3 ubiquitylation, initiating with ubiquitin linked to the E2 enzyme UBE2L3, then transferred to the catalytic cysteine of ARIH1, and culminating in ubiquitin linkage to a substrate bound to the SCF E3 ligase. The E3-E3 mechanism places the ubiquitin-linked active site of ARIH1 adjacent to substrates bound to F-box proteins (for example, substrates with folded structures or limited length) that are incompatible with previously described conventional RING E3-only mechanisms. The versatile E3-E3 super-assembly may therefore underlie widespread ubiquitylation. | |||||||||
履歴 |
|
-構造の表示
ムービー |
ムービービューア |
---|---|
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 | 7b5m.cif.gz | 301.7 KB | 表示 | PDBx/mmCIF形式 |
---|---|---|---|---|
PDB形式 | pdb7b5m.ent.gz | 238.8 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 7b5m.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 | 7b5m_validation.pdf.gz | 912.7 KB | 表示 | wwPDB検証レポート |
---|---|---|---|---|
文書・詳細版 | 7b5m_full_validation.pdf.gz | 940.1 KB | 表示 | |
XML形式データ | 7b5m_validation.xml.gz | 60.6 KB | 表示 | |
CIF形式データ | 7b5m_validation.cif.gz | 89.8 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/b5/7b5m ftp://data.pdbj.org/pub/pdb/validation_reports/b5/7b5m | HTTPS FTP |
-関連構造データ
-リンク
-集合体
登録構造単位 |
|
---|---|
1 |
|
-要素
-タンパク質 , 2種, 2分子 CU
#1: 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: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: Q13616 |
---|---|
#6: タンパク質 | 分子量: 8519.778 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 |
-E3 ubiquitin-protein ligase ... , 2種, 2分子 HR
#2: タンパク質 | 分子量: 64005.605 Da / 分子数: 1 / Mutation: F430A, E431A, E503A / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ARIH1, ARI, MOP6, UBCH7BP, HUSSY-27 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q9Y4X5, RBR-type E3 ubiquitin transferase |
---|---|
#7: タンパク質 | 分子量: 12289.977 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: RBX1, RNF75, ROC1 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) 参照: UniProt: P62877, RING-type E3 ubiquitin transferase, cullin-RING-type E3 NEDD8 transferase |
-S-phase kinase-associated protein ... , 2種, 2分子 TS
#3: タンパク質 | 分子量: 47817.785 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: SKP2, FBXL1 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q13309 |
---|---|
#5: タンパク質 | 分子量: 18679.965 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: SKP1, EMC19, OCP2, SKP1A, TCEB1L / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P63208 |
-Cyclin-dependent ... , 2種, 2分子 KP
#4: タンパク質 | 分子量: 9679.211 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: CKS1B, CKS1, PNAS-143, PNAS-16 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P61024 |
---|---|
#8: タンパク質 | 分子量: 22185.262 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: CDKN1B, KIP1 / 発現宿主: synthetic construct (人工物) / 参照: UniProt: P46527 |
-非ポリマー , 1種, 5分子
#9: 化合物 | ChemComp-ZN / |
---|
-詳細
研究の焦点であるリガンドがあるか | N |
---|
-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
---|---|
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 |
| ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
分子量 | 値: 0.25 MDa | ||||||||||||||||||||||||||||||
由来(天然) |
| ||||||||||||||||||||||||||||||
由来(組換発現) |
| ||||||||||||||||||||||||||||||
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 |
-電子顕微鏡撮影
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
---|---|
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 e/Å2 フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) |
-解析
ソフトウェア | 名称: PHENIX / バージョン: 1.18.2_3874: / 分類: 精密化 | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3次元再構成 | 解像度: 3.91 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 759489 / 対称性のタイプ: POINT | ||||||||||||||||||||||||
拘束条件 |
|