- PDB-2mbq: K11-linked Diubiquitin average solution structure at pH 6.8, 150 ... -
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Basic information
Entry
Database: PDB / ID: 2mbq
Title
K11-linked Diubiquitin average solution structure at pH 6.8, 150 mM NaCl
Components
Ubiquitin
Keywords
SIGNALING PROTEIN / diubiquitin / K11
Function / homology
Function and homology information
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 ...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 / 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 / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / 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 / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / 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 / 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 / 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 / AUF1 (hnRNP D0) binds and destabilizes mRNA / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / 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 / Negative regulation of FGFR3 signaling / Hh mutants are degraded by ERAD / Recognition of DNA damage by PCNA-containing replication complex / Peroxisomal protein import / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Regulation of TNFR1 signaling / Negative regulation of FGFR2 signaling / Termination of translesion DNA synthesis / Negative regulation of FGFR4 signaling / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / Stabilization of p53 / EGFR downregulation / Negative regulation of NOTCH4 signaling / Negative regulation of FGFR1 signaling / Iron uptake and transport / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / G2/M Checkpoints / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Vif-mediated degradation of APOBEC3G Similarity search - Function
Mass: 8576.831 Da / Num. of mol.: 2 / Fragment: UNP residues 1-76 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pJY2 / References: UniProt: P0CG48
Sequence details
DISTAL UBIQUITIN (CHAIN A) AND PROXIMAL UBIQUITIN (CHAIN B) ARE CONNECTED VIA A COVALENT LINKAGE ...DISTAL UBIQUITIN (CHAIN A) AND PROXIMAL UBIQUITIN (CHAIN B) ARE CONNECTED VIA A COVALENT LINKAGE BETWEEN C GLY 76 OF CHAIN A AND NZ LYS 11 OF CHAIN B. THIS LINKAGE HAS NOT BEEN MODELED IN THIS STRUCTURE.
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Experimental details
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Experiment
Experiment
Method: SOLUTION NMR
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Type
1
1
1
2D 1H-15N HSQC
1
2
1
2D 1H-15N IPAPHSQC
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Sample preparation
Details
Contents: 75 uM [U-99% 15N] ubiquitin, 20 mM sodium phosphate, 150 mM sodium chloride, 93% H2O/7% D2O Solvent system: 93% H2O/7% D2O
Type: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz
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Processing
NMR software
Name
Version
Developer
Classification
TopSpin
2.1
BrukerBiospin
collection
NMRPipe
Delaglio, Grzesiek, Vuister, Zhu, PfeiferandBax
processing
Sparky
Goddard
chemicalshiftassignment
in-house
refinement
Refinement
Method: in-house RDC (orientation), MTSL (distance) / Software ordinal: 1 Details: Ub/Ub orientation determined from RDCs via alignment tensors, and Z-distance refined using site-directed spin labeling distance constraints (MTSL on distal position 36) from 0 mM NaCl ...Details: Ub/Ub orientation determined from RDCs via alignment tensors, and Z-distance refined using site-directed spin labeling distance constraints (MTSL on distal position 36) from 0 mM NaCl structure. No MTSL data was collected at 150 mM NaCl.
NMR representative
Selection criteria: closest to the average
NMR ensemble
Conformer selection criteria: target function / Conformers calculated total number: 1 / Conformers submitted total number: 1
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