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Yorodumi- PDB-2k8c: Solution structure of PLAA family ubiquitin binding domain (PFUC)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2k8c | ||||||
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Title | Solution structure of PLAA family ubiquitin binding domain (PFUC) trans isomer in complex with ubiquitin | ||||||
Components |
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Keywords | PROTEIN BINDING / Ubiquitin in complex with PFUC trans isomer / Cytoplasm / Nucleus / Phosphoprotein / Ubl conjugation / WD repeat | ||||||
Function / homology | Function and homology information positive regulation of synaptic vesicle recycling / positive regulation of phospholipase A2 activity / negative regulation of protein K63-linked ubiquitination / : / : / ubiquitin recycling / protein modification process => GO:0036211 / phospholipase A2 activator activity / positive regulation of neuron migration / positive regulation of dendrite extension ...positive regulation of synaptic vesicle recycling / positive regulation of phospholipase A2 activity / negative regulation of protein K63-linked ubiquitination / : / : / ubiquitin recycling / protein modification process => GO:0036211 / phospholipase A2 activator activity / positive regulation of neuron migration / positive regulation of dendrite extension / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / prostaglandin metabolic process / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / phospholipid metabolic process / 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 / Constitutive Signaling by NOTCH1 HD Domain Mutants / NOTCH2 Activation and Transmission of Signal to the Nucleus / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Regulation of FZD by ubiquitination / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / InlA-mediated entry of Listeria monocytogenes into host cells / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / Translesion synthesis by REV1 / NF-kB is activated and signals survival / Regulation of PTEN localization / Translesion synthesis by POLK / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / cytosolic ribosome / Josephin domain DUBs / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / 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 / 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 / Regulation of NF-kappa B signaling / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / Negative regulators of DDX58/IFIH1 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Fu, Q.S. / Zhou, C.J. / Gao, H.C. / Lin, D.H. / Hu, H.Y. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Structural Basis for Ubiquitin Recognition by a Novel Domain from Human Phospholipase A2-activating Protein. Authors: Fu, Q.S. / Zhou, C.J. / Gao, H.C. / Jiang, Y.J. / Zhou, Z.R. / Hong, J. / Yao, W.M. / Song, A.X. / Lin, D.H. / Hu, H.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2k8c.cif.gz | 529.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2k8c.ent.gz | 465.1 KB | Display | PDB format |
PDBx/mmJSON format | 2k8c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k8/2k8c ftp://data.pdbj.org/pub/pdb/validation_reports/k8/2k8c | HTTPS FTP |
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-Related structure data
-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.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RPS27A, UBA80, UBCEP1, UBA52, UBCEP2, UBB, UBC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62988, UniProt: P0CG48*PLUS |
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#2: Protein | Mass: 9032.011 Da / Num. of mol.: 1 / Fragment: UNP residues 386-465 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PLAA, PLAP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y263 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 50mM NaCl / pH: 6.5 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Varian Unity / Manufacturer: Varian / Model: UNITY / Field strength: 600 MHz |
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-Processing
NMR software | Name: CNS / Developer: Brunger, Adams, Clore, Gros, Nilges and Read / Classification: refinement |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: The structures were calculated with HADDOCK by NMR restraint-guided docking |
NMR representative | Selection criteria: lowest energy |
NMR ensemble | Conformer selection criteria: 10 structures for lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 10 |