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

Basic information

Entry

Database: SASBDB / ID: SASDCG7

Sample

Lys63-linked diubiquitin at pH7.4

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

Function / homology

Function:

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 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / 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 / TICAM1,TRAF6-dependent induction of TAK1 complex / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Constitutive Signaling by NOTCH1 HD Domain Mutants / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / Regulation of FZD by ubiquitination / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / VLDLR internalisation and degradation / Pexophagy / 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 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by POLK / 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 / InlB-mediated entry of Listeria monocytogenes into host cell / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / IKK complex recruitment mediated by RIP1 / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / Regulation of NF-kappa B signaling / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / activated TAK1 mediates p38 MAPK activation / TNFR2 non-canonical NF-kB pathway / Negative regulators of DDX58/IFIH1 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Deactivation of the beta-catenin transactivating complex / Regulation of signaling by CBL / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / Fanconi Anemia Pathway / Negative regulation of FGFR3 signaling / Peroxisomal protein import / Hh mutants are degraded by ERAD / Degradation of AXIN / Stabilization of p53 / Recognition of DNA damage by PCNA-containing replication complex / Regulation of TNFR1 signaling / Activation of NF-kappaB in B cells / Negative regulation of FGFR2 signaling / EGFR downregulation / Degradation of GLI1 by the proteasome / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Termination of translesion DNA synthesis / Negative regulation of FGFR4 signaling / Hedgehog ligand biogenesis / G2/M Checkpoints / Negative regulation of FGFR1 signaling / Defective CFTR causes cystic fibrosis / Iron uptake and transport / Negative regulation of NOTCH4 signaling

Domain/homology:

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

Component:

Polyubiquitin-C

• Biological species: Homo sapiens (human)
• Citation: Journal: Biochemistry / Year: 2018; Title: Characterizing Protein Dynamics with Integrative Use of Bulk and Single-Molecule Techniques.; Authors: Zhu Liu / Zhou Gong / Yong Cao / Yue-He Ding / Meng-Qiu Dong / Yun-Bi Lu / Wei-Ping Zhang / Chun Tang / ; Abstract: 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.

Contact author

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

Models

Sample

• Sample: Name: Lys63-linked diubiquitin at pH7.4 / Specimen concentration: 2.6 mg/ml
• Buffer: Name: 20mM HEPES, 150mM NaCl / pH: 7.4

Entity #757

Name: ubiquitin / Type: protein / Description: Polyubiquitin-C / Formula weight: 8.565 / Num. of mol.: 2 / Source: Homo sapiens / References: UniProt: P0CG48
Sequence:

MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGG

Experimental information

• Beam: Instrument name: Shanghai Synchrotron Radiation Facility (SSRF) BL19U2; City: Shanghai / 国: China / Type of source: X-ray synchrotron / Wavelength: 0.1033 Å / Dist. spec. to detc.: 2.1 mm
• Detector: Name: Pilatus 1M

Scan

Title: Lys63-linked diubiquitin at pH7.4 / Measurement date: Mar 24, 2016 / Storage temperature: 25 °C / Cell temperature: 25 °C / Exposure time: 1 sec. / Number of frames: 20 / Unit: 1/A /

	Min	Max
Q	0.0197	0.4611

Distance distribution function P(R)

Sofotware P(R): GNOM 5.0 / Number of points: 497 /

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

Result

Type of curve: single_conc /

	Experimental	Porod
MW	13 kDa	13 kDa
Volume	-	22 nm3

	P(R)	P(R) error	Guinier	Guinier error
Forward scattering, I0	66.4	0.56	63.25	1.64
Radius of gyration, Rg	2.1 nm	0.01	2 nm	0.15

	Min	Max
D	-	7
Guinier point	4	55