+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 8or0 | |||||||||||||||
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タイトル | CAND1-CUL1-RBX1-SKP1-SKP2-CKS1-CDK2 | |||||||||||||||
要素 |
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キーワード | LIGASE (リガーゼ) / CAND1 / substrate receptor exchange factor / cullin-RING ligase / CRL / SCF / neddylation / DCNL1 co-E3 / ubiquitin signaling | |||||||||||||||
機能・相同性 | 機能・相同性情報 SCF complex assembly / positive regulation of protein polyubiquitination / Parkin-FBXW7-Cul1 ubiquitin ligase complex / F-box domain binding / Aberrant regulation of mitotic exit in cancer due to RB1 defects / PcG protein complex / negative regulation of catalytic activity / cullin-RING-type E3 NEDD8 transferase / cellular response to chemical stress / NEDD8 transferase activity ...SCF complex assembly / positive regulation of protein polyubiquitination / Parkin-FBXW7-Cul1 ubiquitin ligase complex / F-box domain binding / Aberrant regulation of mitotic exit in cancer due to RB1 defects / PcG protein complex / negative regulation of catalytic activity / cullin-RING-type E3 NEDD8 transferase / cellular response to chemical stress / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / mitotic cell cycle phase transition / Cul7-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / positive regulation of ubiquitin protein ligase activity / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / maintenance of protein location in nucleus / positive regulation of protein autoubiquitination / protein neddylation / cyclin-dependent protein serine/threonine kinase activator activity / NEDD8 ligase activity / Cul5-RING ubiquitin ligase complex / ubiquitin-ubiquitin ligase activity / Cul4A-RING E3 ubiquitin ligase complex / SCF複合体 / Cul2-RING ubiquitin ligase complex / positive regulation of intracellular estrogen receptor signaling pathway / negative regulation of type I interferon production / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Cul3-RING ubiquitin ligase complex / cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / cyclin E1-CDK2 complex / cyclin A2-CDK2 complex / positive regulation of DNA-templated DNA replication initiation / G2期 / cyclin-dependent protein kinase activity / Y染色体 / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / positive regulation of heterochromatin formation / p53-Dependent G1 DNA Damage Response / Prolactin receptor signaling / X染色体 / PTK6 Regulates Cell Cycle / regulation of anaphase-promoting complex-dependent catabolic process / protein monoubiquitination / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / centriole replication / cullin family protein binding / Regulation of APC/C activators between G1/S and early anaphase / centrosome duplication / Telomere Extension By Telomerase / G0 and Early G1 / ubiquitin-like ligase-substrate adaptor activity / Activation of the pre-replicative complex / cyclin-dependent protein kinase holoenzyme complex / cellular response to nitric oxide / Nuclear events stimulated by ALK signaling in cancer / positive regulation of RNA polymerase II transcription preinitiation complex assembly / サイクリン依存性キナーゼ / protein K48-linked ubiquitination / cyclin-dependent protein serine/threonine kinase activity / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / カハール体 / Activation of ATR in response to replication stress / Cyclin E associated events during G1/S transition / Cyclin A/B1/B2 associated events during G2/M transition / Cyclin A:Cdk2-associated events at S phase entry / ubiquitin ligase complex / condensed chromosome / mitotic G1 DNA damage checkpoint signaling / positive regulation of TORC1 signaling / regulation of mitotic cell cycle / regulation of G2/M transition of mitotic cell cycle / TBP-class protein binding / Regulation of BACH1 activity / T細胞 / cyclin binding / post-translational protein modification / MAP3K8 (TPL2)-dependent MAPK1/3 activation / intrinsic apoptotic signaling pathway / response to organic substance / meiotic cell cycle / ubiquitin binding / positive regulation of DNA replication / SCF-beta-TrCP mediated degradation of Emi1 / male germ cell nucleus / molecular function activator activity / NIK-->noncanonical NF-kB signaling / Vpu mediated degradation of CD4 / Degradation of DVL / Dectin-1 mediated noncanonical NF-kB signaling / Recognition of DNA damage by PCNA-containing replication complex / cellular response to amino acid stimulus / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Negative regulation of NOTCH4 signaling / animal organ morphogenesis 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: 3.1 Å | |||||||||||||||
データ登録者 | Shaaban, M. / Clapperton, J.A. / Ding, S. / Maeots, M.E. / Enchev, R.I. | |||||||||||||||
資金援助 | 英国, 4件
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引用 | ジャーナル: Mol Cell / 年: 2023 タイトル: Structural and mechanistic insights into the CAND1-mediated SCF substrate receptor exchange. 著者: Mohammed Shaaban / Julie A Clapperton / Shan Ding / Simone Kunzelmann / Märt-Erik Mäeots / Sarah L Maslen / J Mark Skehel / Radoslav I Enchev / 要旨: Modular SCF (SKP1-CUL1-Fbox) ubiquitin E3 ligases orchestrate multiple cellular pathways in eukaryotes. Their variable SKP1-Fbox substrate receptor (SR) modules enable regulated substrate recruitment ...Modular SCF (SKP1-CUL1-Fbox) ubiquitin E3 ligases orchestrate multiple cellular pathways in eukaryotes. Their variable SKP1-Fbox substrate receptor (SR) modules enable regulated substrate recruitment and subsequent proteasomal degradation. CAND proteins are essential for the efficient and timely exchange of SRs. To gain structural understanding of the underlying molecular mechanism, we reconstituted a human CAND1-driven exchange reaction of substrate-bound SCF alongside its co-E3 ligase DCNL1 and visualized it by cryo-EM. We describe high-resolution structural intermediates, including a ternary CAND1-SCF complex, as well as conformational and compositional intermediates representing SR- or CAND1-dissociation. We describe in molecular detail how CAND1-induced conformational changes in CUL1/RBX1 provide an optimized DCNL1-binding site and reveal an unexpected dual role for DCNL1 in CAND1-SCF dynamics. Moreover, a partially dissociated CAND1-SCF conformation accommodates cullin neddylation, leading to CAND1 displacement. Our structural findings, together with functional biochemical assays, help formulate a detailed model for CAND-SCF regulation. | |||||||||||||||
履歴 |
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-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
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-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 8or0.cif.gz | 495.6 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb8or0.ent.gz | 383.3 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 8or0.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
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/or/8or0 ftp://data.pdbj.org/pub/pdb/validation_reports/or/8or0 | HTTPS FTP |
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-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 ABC
#1: タンパク質 | 分子量: 93730.672 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: Spodoptera frugiperda (ツマジロクサヨトウ) 参照: UniProt: Q13616 |
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#2: 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: Spodoptera frugiperda (ツマジロクサヨトウ) 参照: UniProt: P62877, RING-type E3 ubiquitin transferase, cullin-RING-type E3 NEDD8 transferase |
#3: タンパク質 | 分子量: 137358.219 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: CAND1, KIAA0829, TIP120, TIP120A / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: Q86VP6 |
-S-phase kinase-associated protein ... , 2種, 2分子 DE
#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 BL21(DE3) (大腸菌) / 参照: UniProt: P63208 |
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#5: タンパク質 | 分子量: 48335.312 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 BL21(DE3) (大腸菌) / 参照: UniProt: Q13309 |
-Cyclin-dependent ... , 2種, 2分子 GH
#6: タンパク質 | 分子量: 8894.114 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 BL21(DE3) (大腸菌) / 参照: UniProt: P61024 |
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#7: タンパク質 | 分子量: 33976.488 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: Spodoptera frugiperda (ツマジロクサヨトウ) 参照: UniProt: P24941, サイクリン依存性キナーゼ |
-非ポリマー , 1種, 3分子
#8: 化合物 |
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-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: CAND1-CUL1-RBX1-SKP1-SKP2-CKS1-CDK2 / タイプ: COMPLEX / 詳細: Ternary complex CAND1-SCF / Entity ID: #1-#7 / 由来: RECOMBINANT | ||||||||||||||||||||
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分子量 | 実験値: NO | ||||||||||||||||||||
由来(天然) | 生物種: Homo sapiens (ヒト) | ||||||||||||||||||||
由来(組換発現) | 生物種: Spodoptera frugiperda, Escherichia coli BL21(DE3) | ||||||||||||||||||||
緩衝液 | pH: 7.5 | ||||||||||||||||||||
緩衝液成分 |
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試料 | 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: GOLD / グリッドのサイズ: 400 divisions/in. / グリッドのタイプ: Quantifoil R1.2/1.3 | ||||||||||||||||||||
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 湿度: 100 % / 凍結前の試料温度: 277.15 K |
-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 FIELDBright-field microscopy / 倍率(公称値): 130000 X / 最大 デフォーカス(公称値): 2500 nm / 最小 デフォーカス(公称値): 700 nm |
撮影 | 電子線照射量: 49.1 e/Å2 フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) |
-解析
CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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対称性 | 点対称性: C1 (非対称) | ||||||||||||||||||||||||
3次元再構成 | 解像度: 3.1 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 1056777 / 対称性のタイプ: POINT | ||||||||||||||||||||||||
拘束条件 |
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