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- PDB-2mjb: Solution nmr structure of ubiquitin refined against dipolar coupl... -

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Basic information

Entry
Database: PDB / ID: 2mjb
TitleSolution nmr structure of ubiquitin refined against dipolar couplings in 4 media
ComponentsUbiquitin-60S ribosomal protein L40
KeywordsSIGNALING 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 / 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 ...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 / Regulation of innate immune responses to cytosolic DNA / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / 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 / Translesion synthesis by POLK / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / 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 / Translesion synthesis by POLI / Regulation of activated PAK-2p34 by proteasome mediated degradation / 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 / Negative regulation of FGFR2 signaling / Stabilization of p53 / Hh mutants are degraded by ERAD
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 ...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-ribosomal protein eL40 fusion protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model1
AuthorsMaltsev, A. / Grishaev, A. / Roche, J. / Zasloff, M. / Bax, A.
CitationJournal: J.Am.Chem.Soc. / Year: 2014
Title: Improved cross validation of a static ubiquitin structure derived from high precision residual dipolar couplings measured in a drug-based liquid crystalline phase.
Authors: Maltsev, A.S. / Grishaev, A. / Roche, J. / Zasloff, M. / Bax, A.
History
DepositionJan 2, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin-60S ribosomal protein L40


Theoretical massNumber of molelcules
Total (without water)8,5771
Polymers8,5771
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)20 / 20all calculated structures submitted
RepresentativeModel #1closest to the average

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Components

#1: Protein Ubiquitin-60S ribosomal protein L40 / 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

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N IPAP HSQC
1222D 1H-15N IPAP HSQC
1312D 1H-15N TROSY HSQC
1422D 1H-15N TROSY HSQC
1513D TROSY HNCO
1623D TROSY HNCO
2733D HN(CO)CA 1H-1H decoupled
2841H-15N ARTSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 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% D2O95% H2O/5% D2O
20.5 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% D2O95% H2O/5% D2O
30.6 mM [U-100% 13C; U-100% 15N] ubiquitin, 13 mg/mL Pf1 phage, 140 mM sodium chloride, 95% H2O/5% D2O95% H2O/5% D2O
40.8 mM [U-100% 13C; U-100% 15N; U-100% 2H] ubiquitin, 14 mg/mL Pf1 phage, 150 mM sodium chloride, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMubiquitin-1[U-100% 13C; U-100% 15N; U-100% 2H]1
20 mMD4-imidazole-2[U-100% 2H]1
4.8 mMsqualamine-31
1.5 mMhexanol-41
10 mMsodium phosphate-51
0.5 mMubiquitin-6[U-100% 13C; U-100% 15N; U-100% 2H]2
20 mMD4-imidazole-7[U-100% 2H]2
1.5 mMhexanol-82
10 mMsodium phosphate-92
0.6 mMubiquitin-10[U-100% 13C; U-100% 15N]3
13 mg/mLPf1 phage-113
140 mMsodium chloride-123
0.8 mMubiquitin-13[U-100% 13C; U-100% 15N; U-100% 2H]4
14 mg/mLPf1 phage-144
150 mMsodium chloride-154
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
16ambient 308 K
26ambient 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE8003

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: 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 constraintsNOE constraints total: 2754 / Protein chi angle constraints total count: 35 / Protein phi angle constraints total count: 64
NMR representativeSelection criteria: closest to the average
NMR ensembleAverage 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 rmsDistance rms dev: 0.024 Å

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