+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 5l9t | ||||||||||||||||||
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タイトル | Model of human Anaphase-promoting complex/Cyclosome (APC/C-CDH1) with E2 UBE2S poised for polyubiquitination where UBE2S, APC2, and APC11 are modeled into low resolution density | ||||||||||||||||||
要素 |
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キーワード | CELL CYCLE / Ubiquitination / multi-protein complex / cell division / conformational regulation | ||||||||||||||||||
機能・相同性 | 機能・相同性情報 protein localization to septin ring / mitotic morphogenesis checkpoint signaling / cellular bud neck septin ring / positive regulation of anaphase-promoting complex-dependent catabolic process / regulation of meiotic nuclear division / protein K27-linked ubiquitination / positive regulation of synapse maturation / free ubiquitin chain polymerization / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / protein K29-linked ubiquitination ...protein localization to septin ring / mitotic morphogenesis checkpoint signaling / cellular bud neck septin ring / positive regulation of anaphase-promoting complex-dependent catabolic process / regulation of meiotic nuclear division / protein K27-linked ubiquitination / positive regulation of synapse maturation / free ubiquitin chain polymerization / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / protein K29-linked ubiquitination / regulation of mitotic cell cycle spindle assembly checkpoint / protein branched polyubiquitination / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / Phosphorylation of Emi1 / anaphase-promoting complex / Aberrant regulation of mitotic exit in cancer due to RB1 defects / regulation of meiotic cell cycle / anaphase-promoting complex-dependent catabolic process / metaphase/anaphase transition of mitotic cell cycle / lens fiber cell differentiation / positive regulation of synaptic plasticity / regulation of exit from mitosis / cellular bud neck / anaphase-promoting complex binding / Phosphorylation of the APC/C / positive regulation of mitotic metaphase/anaphase transition / protein K6-linked ubiquitination / positive regulation of ubiquitin protein ligase activity / ubiquitin ligase activator activity / protein K11-linked ubiquitination / enzyme-substrate adaptor activity / hypothalamus gonadotrophin-releasing hormone neuron development / positive regulation of dendrite morphogenesis / regulation of mitotic metaphase/anaphase transition / female meiosis I / positive regulation of protein monoubiquitination / ubiquitin-ubiquitin ligase activity / exit from mitosis / mitochondrion transport along microtubule / fat pad development / mitotic metaphase chromosome alignment / E2 ubiquitin-conjugating enzyme / female gonad development / seminiferous tubule development / male meiosis I / negative regulation of cellular senescence / mitotic G2 DNA damage checkpoint signaling / Regulation of APC/C activators between G1/S and early anaphase / cullin family protein binding / ubiquitin conjugating enzyme activity / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / protein K63-linked ubiquitination / Transcriptional Regulation by VENTX / ubiquitin-like ligase-substrate adaptor activity / positive regulation of axon extension / protein K48-linked ubiquitination / regulation of neuron apoptotic process / heterochromatin / regulation of proteasomal protein catabolic process / Cyclin A:Cdk2-associated events at S phase entry / energy homeostasis / Maturation of protein E / 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 / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Prevention of phagosomal-lysosomal fusion / Glycogen synthesis / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Endosomal Sorting Complex Required For Transport (ESCRT) / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / TICAM1,TRAF6-dependent induction of TAK1 complex / Membrane binding and targetting of GAG proteins / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of FZD by ubiquitination / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / p75NTR recruits signalling complexes / APC/C:Cdc20 mediated degradation of Cyclin B / VLDLR internalisation and degradation / Downregulation of ERBB4 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / InlA-mediated entry of Listeria monocytogenes into host cells / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Pexophagy 類似検索 - 分子機能 | ||||||||||||||||||
生物種 | Homo sapiens (ヒト) Saccharomyces cerevisiae (パン酵母) | ||||||||||||||||||
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: 6.4 Å | ||||||||||||||||||
データ登録者 | Brown, N.G. / VanderLinden, R. / Dube, P. / Haselbach, D. / Peters, J.M. / Stark, H. / Schulman, B.A. | ||||||||||||||||||
資金援助 | 米国, ドイツ, 5件
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引用 | ジャーナル: Cell / 年: 2016 タイトル: Dual RING E3 Architectures Regulate Multiubiquitination and Ubiquitin Chain Elongation by APC/C. 著者: Nicholas G Brown / Ryan VanderLinden / Edmond R Watson / Florian Weissmann / Alban Ordureau / Kuen-Phon Wu / Wei Zhang / Shanshan Yu / Peter Y Mercredi / Joseph S Harrison / Iain F Davidson / ...著者: Nicholas G Brown / Ryan VanderLinden / Edmond R Watson / Florian Weissmann / Alban Ordureau / Kuen-Phon Wu / Wei Zhang / Shanshan Yu / Peter Y Mercredi / Joseph S Harrison / Iain F Davidson / Renping Qiao / Ying Lu / Prakash Dube / Michael R Brunner / Christy R R Grace / Darcie J Miller / David Haselbach / Marc A Jarvis / Masaya Yamaguchi / David Yanishevski / Georg Petzold / Sachdev S Sidhu / Brian Kuhlman / Marc W Kirschner / J Wade Harper / Jan-Michael Peters / Holger Stark / Brenda A Schulman / 要旨: Protein ubiquitination involves E1, E2, and E3 trienzyme cascades. E2 and RING E3 enzymes often collaborate to first prime a substrate with a single ubiquitin (UB) and then achieve different forms of ...Protein ubiquitination involves E1, E2, and E3 trienzyme cascades. E2 and RING E3 enzymes often collaborate to first prime a substrate with a single ubiquitin (UB) and then achieve different forms of polyubiquitination: multiubiquitination of several sites and elongation of linkage-specific UB chains. Here, cryo-EM and biochemistry show that the human E3 anaphase-promoting complex/cyclosome (APC/C) and its two partner E2s, UBE2C (aka UBCH10) and UBE2S, adopt specialized catalytic architectures for these two distinct forms of polyubiquitination. The APC/C RING constrains UBE2C proximal to a substrate and simultaneously binds a substrate-linked UB to drive processive multiubiquitination. Alternatively, during UB chain elongation, the RING does not bind UBE2S but rather lures an evolving substrate-linked UB to UBE2S positioned through a cullin interaction to generate a Lys11-linked chain. Our findings define mechanisms of APC/C regulation, and establish principles by which specialized E3-E2-substrate-UB architectures control different forms of polyubiquitination. | ||||||||||||||||||
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 | 5l9t.cif.gz | 365.2 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb5l9t.ent.gz | 203.4 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 5l9t.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 | 5l9t_validation.pdf.gz | 1 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 5l9t_full_validation.pdf.gz | 1 MB | 表示 | |
XML形式データ | 5l9t_validation.xml.gz | 88 KB | 表示 | |
CIF形式データ | 5l9t_validation.cif.gz | 135.9 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/l9/5l9t ftp://data.pdbj.org/pub/pdb/validation_reports/l9/5l9t | 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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-要素
-Anaphase-promoting complex subunit ... , 11種, 13分子 ABDEGWILMNOXY
#1: タンパク質 | 分子量: 216725.469 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: ANAPC1, TSG24 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: Q9H1A4 | ||||||||||||
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#2: タンパク質 | 分子量: 9854.647 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: ANAPC11, HSPC214 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: Q9NYG5 | ||||||||||||
#4: タンパク質 | 分子量: 14286.727 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: ANAPC15, C11orf51, HSPC020 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: P60006 | ||||||||||||
#5: タンパク質 | 分子量: 11677.995 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: ANAPC16, C10orf104, CENP-27 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: Q96DE5 | ||||||||||||
#7: タンパク質 | 分子量: 9793.999 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CDC26, ANAPC12, C9orf17 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: Q8NHZ8 #8: タンパク質 | | 分子量: 93207.328 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: ANAPC4, APC4 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: Q9UJX5 #10: タンパク質 | | 分子量: 21282.143 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: ANAPC10, APC10 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: Q9UM13 #11: タンパク質 | | 分子量: 8528.309 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: ANAPC13 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: Q9BS18 #12: タンパク質 | | 分子量: 93938.977 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: ANAPC2, APC2, KIAA1406 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: Q9UJX6 #13: タンパク質 | | 分子量: 85179.766 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: ANAPC5, APC5 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: Q9UJX4 #17: タンパク質 | 分子量: 63204.020 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ANAPC7, APC7 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: Q9UJX3 |
-Cell division cycle protein ... , 3種, 6分子 CPFHJK
#3: タンパク質 | 分子量: 68921.031 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CDC23, ANAPC8 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q9UJX2 #6: タンパク質 | 分子量: 91973.125 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CDC27, ANAPC3, D0S1430E, D17S978E / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: P30260 #9: タンパク質 | 分子量: 71747.516 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CDC16, ANAPC6 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: Q13042 |
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-タンパク質 , 3種, 3分子 RST
#14: タンパク質 | 分子量: 54838.688 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: FZR1, CDH1, FYR, FZR, KIAA1242 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: Q9UM11 |
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#15: タンパク質 | 分子量: 12030.880 Da / 分子数: 1 / 由来タイプ: 組換発現 詳細: This construct comprises a Ubiquitin variant(UBV) fused to APC/C substrate Hsl1 residues 818-842 由来: (組換発現) Homo sapiens (ヒト), (組換発現) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母) 遺伝子: UBB, HSL1, YKL101W, YKL453 / 株: ATCC 204508 / S288c / 発現宿主: Escherichia coli (大腸菌) 参照: UniProt: P0CG47, UniProt: P34244, non-specific serine/threonine protein kinase |
#16: タンパク質 | 分子量: 20519.662 Da / 分子数: 1 / Mutation: C118F, delta 161-201 / 由来タイプ: 組換発現 詳細: This construct as an N-terminal remnant of cleavage site and linker. C95 of this construct is cross-linked to UBv K11C and UB G75C via TMEA. 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: UBE2S, E2EPF, OK/SW-cl.73 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q16763, E2 ubiquitin-conjugating enzyme |
-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: Multi-protein complex of APC/C, coactivator CDH1, and cross-linked complex comprising UBE2S, Ubiquitin, Ubiquitin_variant-substrate (HSL1) fusion. タイプ: COMPLEX 詳細: Due to the low resolution of electron density corresponding to the APC11-APC2 catalytic core and cross linked substrate-Ubiquitin variant-UBE2S complex, these regions are included in the ...詳細: Due to the low resolution of electron density corresponding to the APC11-APC2 catalytic core and cross linked substrate-Ubiquitin variant-UBE2S complex, these regions are included in the coordinates as representative of domain-domain interactions, but their precise relative positions are approximate and not definitive. Entity ID: all / 由来: MULTIPLE SOURCES |
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分子量 | 値: 1.28 MDa / 実験値: NO |
緩衝液 | pH: 8 |
試料 | 濃度: 0.1 mg/ml / 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: SPOT SCAN |
電子レンズ | モード: BRIGHT FIELD |
撮影 | 電子線照射量: 40 e/Å2 フィルム・検出器のモデル: FEI FALCON II (4k x 4k) |
-解析
EMソフトウェア |
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||
3次元再構成 | 解像度: 6.4 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 135578 / 対称性のタイプ: POINT |