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Yorodumi- PDB-2lvq: gp78CUE domain bound to the proximal ubiquitin of K48-linked diub... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2lvq | ||||||
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Title | gp78CUE domain bound to the proximal ubiquitin of K48-linked diubiquitin | ||||||
Components |
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Keywords | SIGNALING PROTEIN/LIGASE / CUE domain / SIGNALING PROTEIN-LIGASE complex | ||||||
Function / homology | Function and homology information regulation of SREBP signaling pathway / RING-type E3 ubiquitin transferase (cysteine targeting) / protein K27-linked ubiquitination / Derlin-1 retrotranslocation complex / BAT3 complex binding / ubiquitin-ubiquitin ligase activity / non-canonical NF-kappaB signal transduction / ubiquitin-specific protease binding / protein K48-linked ubiquitination / protein autoubiquitination ...regulation of SREBP signaling pathway / RING-type E3 ubiquitin transferase (cysteine targeting) / protein K27-linked ubiquitination / Derlin-1 retrotranslocation complex / BAT3 complex binding / ubiquitin-ubiquitin ligase activity / non-canonical NF-kappaB signal transduction / ubiquitin-specific protease binding / protein K48-linked ubiquitination / protein autoubiquitination / ERAD pathway / ubiquitin ligase complex / endoplasmic reticulum unfolded protein response / 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 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / 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 / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / APC-Cdc20 mediated degradation of Nek2A / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / PINK1-PRKN Mediated Mitophagy / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / Regulation of PTEN localization / NRIF signals cell death from the nucleus / Regulation of BACH1 activity / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by REV1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLK / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / EGFR downregulation / 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 / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / ubiquitin binding / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / CDK-mediated phosphorylation and removal of Cdc6 / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Hh mutants are degraded by ERAD / Negative regulation of FGFR3 signaling / SCF(Skp2)-mediated degradation of p27/p21 / Degradation of AXIN Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | lowest energy, model 1 | ||||||
Authors | Liu, S. / Chen, Y. / Huang, T. / Tarasov, S.G. / King, A. / Li, J. / Weissman, A.M. / Byrd, R.A. / Das, R. | ||||||
Citation | Journal: Structure / Year: 2012 Title: Promiscuous Interactions of gp78 E3 Ligase CUE Domain with Polyubiquitin Chains. Authors: Liu, S. / Chen, Y. / Li, J. / Huang, T. / Tarasov, S. / King, A. / Weissman, A.M. / Byrd, R.A. / Das, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2lvq.cif.gz | 1.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2lvq.ent.gz | 1.3 MB | Display | PDB format |
PDBx/mmJSON format | 2lvq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2lvq_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 2lvq_full_validation.pdf.gz | 40 MB | Display | |
Data in XML | 2lvq_validation.xml.gz | 2.5 MB | Display | |
Data in CIF | 2lvq_validation.cif.gz | 2.8 MB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lv/2lvq ftp://data.pdbj.org/pub/pdb/validation_reports/lv/2lvq | HTTPS FTP |
-Related structure data
Related structure data | 2lvnC 2lvoC 2lvpC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 8576.831 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG48 #2: Protein | | Mass: 5966.752 Da / Num. of mol.: 1 / Fragment: CUE domain residues 453-504 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AMFR, RNF45 / Production host: Escherichia coli (E. coli) References: UniProt: Q9UKV5, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 50 mM TRIS, 50 mM sodium chloride, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | |||||||||
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Sample |
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Sample conditions | pH: 7.2 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 / Details: HADDOCK STRUCTURE CALCULATION | ||||||||||||||||||
NMR constraints | NOE constraints total: 42 / NOE long range total count: 42 | ||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 24 / Maximum lower distance constraint violation: 1.8 Å / Maximum upper distance constraint violation: 8 Å | ||||||||||||||||||
NMR ensemble rms | Distance rms dev: 0 Å |