- PDB-2mjb: Solution nmr structure of ubiquitin refined against dipolar coupl... -
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Basic information
Entry
Database: PDB / ID: 2mjb
Title
Solution nmr structure of ubiquitin refined against dipolar couplings in 4 media
Components
Ubiquitin-60S ribosomal protein L40
Keywords
SIGNALING PROTEIN / RESIDUAL DIPOLAR COUPLING / SQUALAMINE
Function / homology
Function and homology information
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 / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Viral mRNA Translation / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit ...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 / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Viral mRNA Translation / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / cytosolic ribosome / 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 Similarity search - Function
Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. ...Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily Similarity search - Domain/homology
Ubiquitin-60SribosomalproteinL40 / CEP52 / Ubiquitin A-52 residue ribosomal protein fusion product 1 / Ubiquitin / 60S ribosomal ...CEP52 / Ubiquitin A-52 residue ribosomal protein fusion product 1 / Ubiquitin / 60S ribosomal protein L40 / Ubiquitin-40S ribosomal protein S27a / Ubiquitin carboxyl extension protein 80 / Ubiquitin / 40S ribosomal protein S27a / Polyubiquitin-B / Ubiquitin / Polyubiquitin-C / Ubiquitin
Mass: 8576.831 Da / Num. of mol.: 1 / Fragment: Ubiquitin-like 3 domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBA52, UBCEP2, RPS27A, UBA80, UBCEP1, UBB, UBC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P62987
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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 IPAPHSQC
1
2
2
2D 1H-15N IPAPHSQC
1
3
1
2D 1H-15N TROSYHSQC
1
4
2
2D 1H-15N TROSYHSQC
1
5
1
3D TROSYHNCO
1
6
2
3D TROSYHNCO
2
7
3
3D HN(CO)CA 1H-1H decoupled
2
8
4
1H-15N ARTSY
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Sample preparation
Details
Solution-ID
Contents
Solvent system
1
0.5 mM [U-100% 13C; U-100% 15N; U-100% 2H] ubiquitin, 20 mM [U-100% 2H] D4-imidazole, 4.8 mM squalamine, 1.5 mM hexanol, 10 mM sodium phosphate, 95% H2O/5% D2O
95% H2O/5% D2O
2
0.5 mM [U-100% 13C; U-100% 15N; U-100% 2H] ubiquitin, 20 mM [U-100% 2H] D4-imidazole, 1.5 mM hexanol, 10 mM sodium phosphate, 95% H2O/5% D2O
95% H2O/5% D2O
3
0.6 mM [U-100% 13C; U-100% 15N] ubiquitin, 13 mg/mL Pf1 phage, 140 mM sodium chloride, 95% H2O/5% D2O
95% H2O/5% D2O
4
0.8 mM [U-100% 13C; U-100% 15N; U-100% 2H] ubiquitin, 14 mg/mL Pf1 phage, 150 mM sodium chloride, 95% H2O/5% D2O
95% H2O/5% D2O
Sample
Conc. (mg/ml)
Component
Isotopic labeling
Solution-ID
0.5mM
ubiquitin-1
[U-100% 13C; U-100% 15N; U-100% 2H]
1
20mM
D4-imidazole-2
[U-100% 2H]
1
4.8mM
squalamine-3
1
1.5mM
hexanol-4
1
10mM
sodium phosphate-5
1
0.5mM
ubiquitin-6
[U-100% 13C; U-100% 15N; U-100% 2H]
2
20mM
D4-imidazole-7
[U-100% 2H]
2
1.5mM
hexanol-8
2
10mM
sodium phosphate-9
2
0.6mM
ubiquitin-10
[U-100% 13C; U-100% 15N]
3
13mg/mL
Pf1 phage-11
3
140mM
sodium chloride-12
3
0.8mM
ubiquitin-13
[U-100% 13C; U-100% 15N; U-100% 2H]
4
14mg/mL
Pf1 phage-14
4
150mM
sodium chloride-15
4
Sample conditions
Conditions-ID
pH
Pressure (kPa)
Temperature (K)
1
6.0
ambient
308K
2
6.0
ambient
298K
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NMR measurement
NMR spectrometer
Type
Manufacturer
Model
Field strength (MHz)
Spectrometer-ID
Bruker Avance
Bruker
AVANCE
500
1
Bruker Avance
Bruker
AVANCE
600
2
Bruker Avance
Bruker
AVANCE
800
3
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Processing
NMR software
Name
Developer
Classification
NMRPipe
Delaglio, Grzesiek, Vuister, Zhu, PfeiferandBax
dataanalysis
X-PLOR NIH
Schwieters, Kuszewski, TjandraandClore
refinement
Refinement
Method: simulated annealing / Software ordinal: 1 Details: Refinement against residual dipolar couplings in 4 alignment media, distance, dihedral angle, and through-H bond (N/C) J-coupling restraints with hydrogen-bonding database potential starting ...Details: Refinement against residual dipolar couplings in 4 alignment media, distance, dihedral angle, and through-H bond (N/C) J-coupling restraints with hydrogen-bonding database potential starting from the coordinates of 1D3Z entry.
NMR constraints
NOE constraints total: 2754 / Protein chi angle constraints total count: 35 / Protein phi angle constraints total count: 64
NMR representative
Selection criteria: closest to the average
NMR ensemble
Average torsion angle constraint violation: 6.9 ° Conformer selection criteria: all calculated structures submitted Conformers calculated total number: 20 / Conformers submitted total number: 20
NMR ensemble rms
Distance rms dev: 0.024 Å
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