+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6sqs | |||||||||
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タイトル | Crystal structure of cat phospho-Ser429 MDM2 RING domain bound to UbcH5B-Ub | |||||||||
要素 |
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キーワード | LIGASE / MDM2 / MDMX / E3 / E2 / ubiquitin ligase / ubiquitin / phosphorylation | |||||||||
機能・相同性 | 機能・相同性情報 regulation of biological quality / (E3-independent) E2 ubiquitin-conjugating enzyme / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / E2 ubiquitin-conjugating enzyme / SARS-CoV-1 modulates host translation machinery / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits ...regulation of biological quality / (E3-independent) E2 ubiquitin-conjugating enzyme / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / E2 ubiquitin-conjugating enzyme / SARS-CoV-1 modulates host translation machinery / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / ubiquitin conjugating enzyme activity / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Viral mRNA Translation / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / protein autoubiquitination / protein K48-linked ubiquitination / cytosolic ribosome / ribonucleoprotein complex binding / ubiquitin ligase complex / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / ubiquitin binding / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / TCF dependent signaling in response to WNT / AUF1 (hnRNP D0) binds and destabilizes mRNA / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL 類似検索 - 分子機能 | |||||||||
生物種 | Felis catus (イエネコ) Homo sapiens (ヒト) | |||||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 1.83 Å | |||||||||
データ登録者 | Magnussen, H.M. / Ahmed, S.F. / Huang, D.T. | |||||||||
資金援助 | 英国, ベルギー, 2件
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引用 | ジャーナル: Nat Commun / 年: 2020 タイトル: Structural basis for DNA damage-induced phosphoregulation of MDM2 RING domain. 著者: Magnussen, H.M. / Ahmed, S.F. / Sibbet, G.J. / Hristova, V.A. / Nomura, K. / Hock, A.K. / Archibald, L.J. / Jamieson, A.G. / Fushman, D. / Vousden, K.H. / Weissman, A.M. / Huang, D.T. | |||||||||
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 | 6sqs.cif.gz | 129.9 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb6sqs.ent.gz | 99.4 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 6sqs.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 | 6sqs_validation.pdf.gz | 421.4 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 6sqs_full_validation.pdf.gz | 421.6 KB | 表示 | |
XML形式データ | 6sqs_validation.xml.gz | 13 KB | 表示 | |
CIF形式データ | 6sqs_validation.cif.gz | 19.7 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/sq/6sqs ftp://data.pdbj.org/pub/pdb/validation_reports/sq/6sqs | 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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単位格子 |
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-要素
#1: タンパク質 | 分子量: 7287.754 Da / 分子数: 2 / 変異: G443T / 由来タイプ: 組換発現 詳細: Residues 422-491 and contains G443T mutation. S429 is phosphorylated. GS at the N-terminus resulted from cloning. 由来: (組換発現) Felis catus (イエネコ) / 遺伝子: MDM2 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q7YRZ8, RING-type E3 ubiquitin transferase #2: タンパク質 | 分子量: 16720.186 Da / 分子数: 2 / 変異: S22R, C85K / 由来タイプ: 組換発現 詳細: Contains S22R and C85K mutations. K85 in Chains B and E form a covalent bond with G76 in Chains C and F, respectively. 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 #3: タンパク質 | 分子量: 8663.908 Da / 分子数: 2 / 由来タイプ: 組換発現 詳細: Contains a GSGGS at the N-terminus resulted from cloning. G76 in Chains C and F form a covalent bond with K85 sidechain in Chains B and E, respectively. 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: RPS27A / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: J3QTR3, UniProt: P62979*PLUS #4: 化合物 | ChemComp-ZN / #5: 水 | ChemComp-HOH / | 研究の焦点であるリガンドがあるか | Y | |
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-実験情報
-実験
実験 | 手法: X線回折 / 使用した結晶の数: 1 |
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-試料調製
結晶 | マシュー密度: 2.43 Å3/Da / 溶媒含有率: 49.43 % |
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結晶化 | 温度: 292 K / 手法: 蒸気拡散法 詳細: 0.1 M Tris-HCl, pH 8.0, 15% (w/v) PEG 2000 MME and 0.1 M KCl |
-データ収集
回折 | 平均測定温度: 100 K / Serial crystal experiment: N |
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放射光源 | 由来: シンクロトロン / サイト: Diamond / ビームライン: I04-1 / 波長: 0.916 Å |
検出器 | タイプ: DECTRIS PILATUS 6M-F / 検出器: PIXEL / 日付: 2018年11月25日 |
放射 | モノクロメーター: 0.916 / プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray |
放射波長 | 波長: 0.916 Å / 相対比: 1 |
反射 | 解像度: 1.83→29.2 Å / Num. obs: 49057 / % possible obs: 95.8 % / 冗長度: 1.8 % / CC1/2: 0.996 / Net I/σ(I): 10.2 |
反射 シェル | 解像度: 1.83→1.88 Å / Num. unique obs: 3293 / CC1/2: 0.539 |
-解析
ソフトウェア |
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精密化 | 構造決定の手法: 分子置換 開始モデル: 5MNJ 解像度: 1.83→29.2 Å / 交差検証法: FREE R-VALUE
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精密化ステップ | サイクル: LAST / 解像度: 1.83→29.2 Å
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