SASDCL6: Lys63-linked dimer ubiquitin (Polyubiquitin-C, ubiquitin)

基本情報

登録情報

データベース: SASBDB / ID: SASDCL6

試料

Lys63-linked dimer ubiquitin

• Polyubiquitin-C (protein), ubiquitin, Homo sapiens

機能・相同性

分子機能:

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) / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Regulation of FZD by ubiquitination / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / Regulation of PTEN localization / VLDLR internalisation and degradation / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / Translesion synthesis by POLI / IKK complex recruitment mediated by RIP1 / Gap-filling DNA repair synthesis and ligation in GG-NER / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / activated TAK1 mediates p38 MAPK activation / Negative regulators of DDX58/IFIH1 signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / NOTCH3 Activation and Transmission of Signal to the Nucleus / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Deactivation of the beta-catenin transactivating complex / Negative regulation of FGFR3 signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / Fanconi Anemia Pathway / Peroxisomal protein import / Degradation of AXIN / Regulation of TNFR1 signaling / Negative regulation of FGFR2 signaling / Stabilization of p53 / Hh mutants are degraded by ERAD / Negative regulation of FGFR4 signaling / Activation of NF-kappaB in B cells / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Negative regulation of FGFR1 signaling / EGFR downregulation / Degradation of GLI1 by the proteasome / Termination of translesion DNA synthesis / Hedgehog ligand biogenesis / G2/M Checkpoints / Defective CFTR causes cystic fibrosis / Recognition of DNA damage by PCNA-containing replication complex / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2

ドメイン・相同性:

: / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily

構成要素:

Polyubiquitin-C

• 生物種: Homo sapiens (ヒト)
• 引用: ジャーナル: Elife / 年: 2015; タイトル: Lys63-linked ubiquitin chain adopts multiple conformational states for specific target recognition.; 著者: Zhu Liu / Zhou Gong / Wen-Xue Jiang / Ju Yang / Wen-Kai Zhu / Da-Chuan Guo / Wei-Ping Zhang / Mai-Li Liu / Chun Tang / ; 要旨: A polyubiquitin comprises multiple covalently linked ubiquitins and recognizes myriad targets. Free or bound to ligands, polyubiquitins are found in different arrangements of ubiquitin subunits. To understand the structural basis for polyubiquitin quaternary plasticity and to explore the target recognition mechanism, we characterize the conformational space of Lys63-linked diubiquitin (K63-Ub2). Refining against inter-subunit paramagnetic NMR data, we show that free K63-Ub2 exists as a dynamic ensemble comprising multiple closed and open quaternary states. The quaternary dynamics enables K63-Ub2 to be specifically recognized in a variety of signaling pathways. When binding to a target protein, one of the preexisting quaternary states is selected and stabilized. A point mutation that shifts the equilibrium between the different states modulates the binding affinities towards K63-Ub2 ligands. This conformational selection mechanism at the quaternary level may be used by polyubiquitins of different lengths and linkages for target recognition.

登録者

• Zhu [e-mail] (Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences)

モデル

試料

• 試料: 名称: Lys63-linked dimer ubiquitin / 試料濃度: 5.1 mg/ml
• バッファ: 名称: 100mM NaCl, 10mM sodium acetate / pH: 6

要素 #757

名称: ubiquitin / タイプ: protein / 記述: Polyubiquitin-C / 分子量: 8.565 / 分子数: 2 / 由来: Homo sapiens / 参照: UniProt: P0CG48
配列:

MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGG

実験情報

• ビーム: 設備名称: Shanghai Synchrotron Radiation Facility (SSRF) BL19U2; 地域: Shanghai / 国: China / 線源: X-ray synchrotron / 波長: 0.1033 Å / スペクトロメータ・検出器間距離: 2.126 mm
• 検出器: 名称: Pilatus 1M

スキャン

タイトル: Lys63-linked dimer ubiquitin / 測定日: 2016年3月24日 / 保管温度: 4 °C / セル温度: 25 °C / 照射時間: 1 sec. / フレーム数: 20 / 単位: 1/A /

	Min	Max
Q	0.0123	0.4699

距離分布関数 P(R)

ソフトウェア P(R): GNOM 5.0 / ポイント数: 410 /

	Min	Max
Q	0.0270648	0.228209
P(R) point	1	410
R	0	65

結果

カーブのタイプ: single_conc /

	実験値	Porod
分子量	14 kDa	14 kDa
体積	-	23.8 nm3

	P(R)	P(R) error	Guinier	Guinier error
前方散乱 I0	69	0.07	69.0664	0.01
慣性半径, Rg	2.115 nm	0.024	2.084 nm	0.01

	Min	Max
D	-	6.5
Guinier point	31	101