+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 7b5r | |||||||||
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タイトル | Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: CUL1-RBX1-SKP1-SKP2-CKSHS1-Cyclin A-CDK2-p27 | |||||||||
要素 |
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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 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 / PTK6 Regulates Cell Cycle / autophagic cell death / Parkin-FBXW7-Cul1 ubiquitin ligase complex / FOXO-mediated transcription of cell cycle genes / F-box domain binding ...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 / PTK6 Regulates Cell Cycle / autophagic cell death / Parkin-FBXW7-Cul1 ubiquitin ligase complex / FOXO-mediated transcription of cell cycle genes / F-box domain binding / negative regulation of epithelial cell proliferation involved in prostate gland development / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / G2 Phase / Phosphorylation of proteins involved in the G2/M transition by Cyclin A:Cdc2 complexes / cyclin A2-CDK1 complex / cyclin A2-CDK2 complex / PcG protein complex / cell cycle G1/S phase transition / Aberrant regulation of mitotic exit in cancer due to RB1 defects / cellular response to luteinizing hormone stimulus / p53-Dependent G1 DNA Damage Response / regulation of cell cycle G1/S phase transition / regulation of exit from mitosis / mitotic cell cycle phase transition / cullin-RING ubiquitin ligase complex / epithelial cell proliferation involved in prostate gland development / negative regulation of epithelial cell apoptotic process / negative regulation of cyclin-dependent protein serine/threonine kinase activity / negative regulation of phosphorylation / Cul7-RING ubiquitin ligase complex / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / positive regulation of ubiquitin protein ligase activity / ubiquitin ligase activator activity / Regulation of APC/C activators between G1/S and early anaphase / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / maintenance of protein location in nucleus / cyclin-dependent protein serine/threonine kinase inhibitor activity / cellular response to leptin stimulus / negative regulation of vascular associated smooth muscle cell proliferation / RHO GTPases activate CIT / male pronucleus / Telomere Extension By Telomerase / G0 and Early G1 / female pronucleus / cyclin-dependent protein serine/threonine kinase activator activity / nuclear export / response to glucagon / cellular response to cocaine / negative regulation of mitotic cell cycle / cellular response to nitric oxide / AKT phosphorylates targets in the cytosol / positive regulation of intracellular estrogen receptor signaling pathway / cyclin-dependent protein serine/threonine kinase regulator activity / Cul4A-RING E3 ubiquitin ligase complex / epithelial cell apoptotic process / SCF ubiquitin ligase complex / cellular response to insulin-like growth factor stimulus / cellular response to antibiotic / Cyclin E associated events during G1/S transition / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / ubiquitin ligase complex scaffold activity / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / negative regulation of kinase activity / positive regulation of DNA biosynthetic process / regulation of cyclin-dependent protein serine/threonine kinase activity / molecular function inhibitor activity / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / cochlea development / cellular response to lithium ion / positive regulation of DNA replication / cellular response to platelet-derived growth factor stimulus / Cyclin A/B1/B2 associated events during G2/M transition / protein kinase inhibitor activity / Prolactin receptor signaling / Cyclin A:Cdk2-associated events at S phase entry / cyclin-dependent protein kinase holoenzyme complex / protein monoubiquitination / regulation of DNA replication / Constitutive Signaling by AKT1 E17K in Cancer / regulation of mitotic cell cycle / regulation of G1/S transition of mitotic cell cycle / cullin family protein binding / inner ear development / protein K63-linked ubiquitination / cellular response to organic cyclic compound / cyclin binding / positive regulation of double-strand break repair via homologous recombination / ubiquitin-like ligase-substrate adaptor activity / response to amino acid / animal organ regeneration / protein K48-linked ubiquitination / post-translational protein modification / Nuclear events stimulated by ALK signaling in cancer / response to glucose / response to cadmium ion / Notch signaling pathway / positive regulation of microtubule polymerization / cellular response to estradiol stimulus / Hsp70 protein binding / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest 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: 3.8 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
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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 |
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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 | 7b5r.cif.gz | 280.6 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb7b5r.ent.gz | 221 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 7b5r.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 | 7b5r_validation.pdf.gz | 953.2 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 7b5r_full_validation.pdf.gz | 982.4 KB | 表示 | |
XML形式データ | 7b5r_validation.xml.gz | 58.7 KB | 表示 | |
CIF形式データ | 7b5r_validation.cif.gz | 86.6 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/b5/7b5r ftp://data.pdbj.org/pub/pdb/validation_reports/b5/7b5r | 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 , 3種, 3分子 CKY
#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: Escherichia coli (大腸菌) / 参照: UniProt: Q13616 |
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#3: 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 |
#6: タンパク質 | 分子量: 48609.574 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: CCNA2, CCN1, CCNA / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P20248 |
-S-phase kinase-associated protein ... , 2種, 2分子 TS
#2: 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 |
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#4: 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 kinase ... , 2種, 2分子 LP
#5: タンパク質 | 分子量: 34056.469 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: CDK2, CDKN2 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P24941, cyclin-dependent kinase |
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#7: タンパク質 | 分子量: 22188.303 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: Escherichia coli (大腸菌) / 参照: UniProt: P46527 |
-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 | 名称: NEDD8-CUL1-RBX1-SKP1-SKP2-CKSHS1-Cyclin A-CDK2-p27-UBE2L3~Ub~ARIH1. Transition State 1 composite map. タイプ: COMPLEX / Entity ID: all / 由来: RECOMBINANT |
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分子量 | 値: 0.30 MDa |
由来(天然) | 生物種: Homo sapiens (ヒト) |
由来(組換発現) | 生物種: Escherichia coli (大腸菌) |
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 |
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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 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 | ||||||||||||||||||||||||
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3次元再構成 | 解像度: 3.8 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 213213 / 対称性のタイプ: POINT | ||||||||||||||||||||||||
拘束条件 |
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