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- PDB-2bgf: NMR structure of Lys48-linked di-ubiquitin using chemical shift p... -

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Basic information

Entry
Database: PDB / ID: 2bgf
TitleNMR structure of Lys48-linked di-ubiquitin using chemical shift perturbation data together with RDCs and 15N-relaxation data
ComponentsDI-UBIQUITIN
KeywordsUBIQUITIN / 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 / cytosolic ribosome / 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 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / 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 / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / 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 / Regulation of PTEN localization / VLDLR internalisation and degradation / 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 / TCF dependent signaling in response to WNT / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / 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 / Degradation of AXIN / Regulation of TNFR1 signaling
Similarity search - Function
Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) ...Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-C / Ubiquitin-60S ribosomal protein L40
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / HADDOCK
AuthorsVan 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
DepositionDec 22, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 31, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 15, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DI-UBIQUITIN
B: DI-UBIQUITIN


Theoretical massNumber of molelcules
Total (without water)17,1542
Polymers17,1542
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200LOWEST ENERGY STRUCTURES OF LOWEST ENERGY CLUSTER
RepresentativeModel #1

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Components

#1: Protein DI-UBIQUITIN / UBIQUITIN


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 detailsFUNCTIONS INCLUDE ATP-DEPENDENT SELECTIVE DEGRADATION OF CELLULAR PROTEINS, MAINTENANCE OF ...FUNCTIONS INCLUDE ATP-DEPENDENT SELECTIVE DEGRADATION OF CELLULAR PROTEINS, MAINTENANCE OF CHROMATIN STRUCTURE, REGULATION OF GENE EXPRESSION, STRESS RESPONSE, AND RIBOSOME BIOGENESIS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HSQC
121TOCSY
NMR detailsText: 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:

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Sample preparation

DetailsContents: 90% WATER/10% D20
Sample conditionsIonic strength: 20 mM / pH: 6.8 / Pressure: 1.0 atm / Temperature: 298.0 K

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NMR measurement

NMR spectrometerType: Bruker OTHER / Manufacturer: Bruker / Model: OTHER / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
HADDOCKDOMINGUEZ, BOELENS,BONVINrefinement
HADDOCKstructure solution
RefinementMethod: 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 ensembleConformer selection criteria: LOWEST ENERGY STRUCTURES OF LOWEST ENERGY CLUSTER
Conformers calculated total number: 200 / Conformers submitted total number: 10

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