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Yorodumi- PDB-2bgf: NMR structure of Lys48-linked di-ubiquitin using chemical shift p... -
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-Basic information
Entry | Database: PDB / ID: 2bgf | ||||||
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Title | NMR structure of Lys48-linked di-ubiquitin using chemical shift perturbation data together with RDCs and 15N-relaxation data | ||||||
Components | DI-UBIQUITIN | ||||||
Keywords | UBIQUITIN / PROTEASOME / DEGRADATION / POLYUBIQUITIN | ||||||
Function / homology | Function and homology information : / : / protein modification process => GO:0036211 / 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 ...: / : / protein modification process => GO:0036211 / 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) / 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 / Endosomal Sorting Complex Required For Transport (ESCRT) / NOTCH2 Activation and Transmission of Signal to the Nucleus / 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 / Regulation of FZD by ubiquitination / 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 / cytosolic ribosome / 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 / 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 / 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 / TNFR2 non-canonical NF-kB pathway / NOTCH3 Activation and Transmission of Signal to the Nucleus / 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 / Recognition of DNA damage by PCNA-containing replication complex / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Hh mutants are degraded by ERAD / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Negative regulation of FGFR3 signaling / Termination of translesion DNA synthesis / Peroxisomal protein import / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | SOLUTION NMR / HADDOCK | ||||||
Authors | Van Dijk, A.D.J. / Fushman, D. / Bonvin, A.M.J.J. | ||||||
Citation | Journal: Proteins: Struct., Funct., Bioinf. / Year: 2005 Title: Various Strategies of Using Residual Dipolar Couplings in NMR-Driven Protein Docking: Application to Lys48-Linked Di-Ubiquitin and Validation Against 15N-Relaxation Data Authors: Van Dijk, A.D.J. / Fushman, D. / Bonvin, A.M.J.J. #1: Journal: J.Mol.Biol. / Year: 2002 Title: Structural Properties of Polyubiquitin Chains in Solution Authors: Varadan, R. / Walker, O. / Pickart, C. / Fushman, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bgf.cif.gz | 525.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bgf.ent.gz | 448.3 KB | Display | PDB format |
PDBx/mmJSON format | 2bgf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bg/2bgf ftp://data.pdbj.org/pub/pdb/validation_reports/bg/2bgf | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar 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.: 2 Source method: isolated from a genetically manipulated source Details: ISOPEPTIDE BOND BETWEEN GLY76A AND LYS48B / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P62988, UniProt: P0CG48*PLUS Compound details | FUNCTIONS INCLUDE ATP-DEPENDENT SELECTIVE DEGRADATION OF CELLULAR PROTEINS, MAINTENANCE OF ...FUNCTIONS INCLUDE ATP-DEPENDENT SELECTIVE DEGRADATIO | |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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NMR details | Text: THE STRUCTURE WAS DETERMINED WITH HADDOCK USING CHEMICAL SHIFT PERTURBATION DATA AS AMBIGUOUS INTERACTION RESTRAINTS AND RESIDUAL DIPOLAR COUPLINGS BOTH AS DIRECT RESTRAINTS (SANI) AND ...Text: THE STRUCTURE WAS DETERMINED WITH HADDOCK USING CHEMICAL SHIFT PERTURBATION DATA AS AMBIGUOUS INTERACTION RESTRAINTS AND RESIDUAL DIPOLAR COUPLINGS BOTH AS DIRECT RESTRAINTS (SANI) AND INTERVECTOR PROJECTION ANGLE RESTRAINTS (VEAN). STRUCTURAL CHARACTERISTICS OF ENSEMBLE OF 10 BEST: AVERAGE (STANDARD DEVIATION) INTERMOLECULAR ENERGIES RAMACHANDRAN ANALYSIS: |
-Sample preparation
Details | Contents: 90% WATER/10% D20 |
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Sample conditions | Ionic strength: 20 mM / pH: 6.8 / Pressure: 1.0 atm / Temperature: 298.0 K |
-NMR measurement
NMR spectrometer | Type: Bruker OTHER / Manufacturer: Bruker / Model: OTHER / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: HADDOCK / Software ordinal: 1 Details: REFINEMENT IS DONE IN EXPLICIT SOLVENT. REFINEMENT AND STRUCTURE CALCULATION DETAILS CAN BE FOUND IN DOMINGUEZ ET AL, JACS 2003, 125, 173 | |||||||||
NMR ensemble | Conformer selection criteria: LOWEST ENERGY STRUCTURES OF LOWEST ENERGY CLUSTER Conformers calculated total number: 200 / Conformers submitted total number: 10 |