SASDCG7: Lys63-linked diubiquitin at pH7.4 (Polyubiquitin-C, ubiquitin)

基本情報

登録情報

データベース: SASBDB / ID: SASDCG7

試料

Lys63-linked diubiquitin at pH7.4

• 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 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / 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 / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / 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 / VLDLR internalisation and degradation / Regulation of PTEN localization / 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 / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / TCF dependent signaling in response to WNT / Asymmetric localization of PCP proteins / Regulation of NF-kappa B signaling / 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 / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Regulation of TNFR1 signaling / Degradation of AXIN / Stabilization of p53 / Hh mutants are degraded by ERAD / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Activation of NF-kappaB in B cells / Negative regulation of FGFR1 signaling / EGFR downregulation / Degradation of GLI1 by the proteasome / Hedgehog ligand biogenesis / Termination of translesion DNA synthesis / G2/M Checkpoints / Defective CFTR causes cystic fibrosis / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Recognition of DNA damage by PCNA-containing replication complex

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: Biochemistry / 年: 2018; タイトル: Characterizing Protein Dynamics with Integrative Use of Bulk and Single-Molecule Techniques.; 著者: Zhu Liu / Zhou Gong / Yong Cao / Yue-He Ding / Meng-Qiu Dong / Yun-Bi Lu / Wei-Ping Zhang / Chun Tang / ; 要旨: A protein dynamically samples multiple conformations, and the conformational dynamics enables protein function. Most biophysical measurements are ensemble-based, with the observables averaged over all members of the ensemble. Though attainable, the decomposition of the observables to the constituent conformational states can be computationally expensive and ambiguous. Here we show that the incorporation of single-molecule fluorescence resonance energy transfer (smFRET) data resolves the ambiguity and affords protein ensemble structures that are more precise and accurate. Using K63-linked diubiquitin, we characterize the dynamic domain arrangements of the model system, with the use of chemical cross-linking coupled with mass spectrometry (CXMS), small-angle X-ray scattering (SAXS), and smFRET techniques. CXMS allows the modeling of protein conformational states that are alternatives to the crystal structure. SAXS provides ensemble-averaged low-resolution shape information. Importantly, smFRET affords state-specific populations, and the FRET distances validate the ensemble structures obtained by refining against CXMS and SAXS restraints. Together, the integrative use of bulk and single-molecule techniques affords better insight into protein dynamics and shall be widely implemented in structural biology.

登録者

• Zhu Liuzhu (Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences)

モデル

試料

• 試料: 名称: Lys63-linked diubiquitin at pH7.4 / 試料濃度: 2.6 mg/ml
• バッファ: 名称: 20mM HEPES, 150mM NaCl / pH: 7.4

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: 2.1 mm
• 検出器: 名称: Pilatus 1M

スキャン

タイトル: Lys63-linked diubiquitin at pH7.4 / 測定日: 2016年3月24日 / 保管温度: 25 °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	0.0197	0.4611

距離分布関数 P(R)

ソフトウェア P(R): GNOM 5.0 / ポイント数: 497 /

	Min	Max
Q	0.0211598	0.265048
P(R) point	1	497
R	0	70

結果

カーブのタイプ: single_conc /

	実験値	Porod
分子量	13 kDa	13 kDa
体積	-	22 nm3

	P(R)	P(R) error	Guinier	Guinier error
前方散乱 I0	66.4	0.56	63.25	1.64
慣性半径, Rg	2.1 nm	0.01	2 nm	0.15

	Min	Max
D	-	7
Guinier point	4	55