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- PDB-2msg: Solid-state NMR structure of ubiquitin -

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Basic information

Entry
Database: PDB / ID: 2msg
TitleSolid-state NMR structure of ubiquitin
ComponentsUbiquitin
KeywordsSIGNALING PROTEIN / UBIQUITIN FOLD
Function / homology
Function and homology information


hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / fat pad development / mitochondrion transport along microtubule / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / regulation of neuron apoptotic process ...hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / fat pad development / mitochondrion transport along microtubule / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic process / energy homeostasis / 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 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / 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 / TICAM1,TRAF6-dependent induction of TAK1 complex / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Constitutive Signaling by NOTCH1 HD Domain Mutants / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / Regulation of FZD by ubiquitination / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / VLDLR internalisation and degradation / Pexophagy / 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 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by POLK / neuron projection morphogenesis / 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 / InlB-mediated entry of Listeria monocytogenes into host cell / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / IKK complex recruitment mediated by RIP1 / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / regulation of mitochondrial membrane potential / positive regulation of protein ubiquitination / TNFR1-induced NF-kappa-B signaling pathway / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / Asymmetric localization of PCP proteins / 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 / activated TAK1 mediates p38 MAPK activation / TNFR2 non-canonical NF-kB pathway / Negative regulators of DDX58/IFIH1 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Deactivation of the beta-catenin transactivating complex / Regulation of signaling by CBL / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / Fanconi Anemia Pathway / Negative regulation of FGFR3 signaling / Peroxisomal protein import / Hh mutants are degraded by ERAD / Degradation of AXIN / Stabilization of p53
Similarity search - Function
: / 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
Biological speciesHomo sapiens (human)
MethodSOLID-STATE NMR / torsion angle dynamics
Model detailsminimized average structure, model1
AuthorsLakomek, N. / Habenstein, B. / Loquet, A. / Shi, C. / Giller, K. / Wolff, S. / Becker, S. / Fasshuber, H. / Lange, A.
CitationJournal: Protein Sci. / Year: 2015
Title: Structural heterogeneity in microcrystalline ubiquitin studied by solid-state NMR.
Authors: Fasshuber, H.K. / Lakomek, N.A. / Habenstein, B. / Loquet, A. / Shi, C. / Giller, K. / Wolff, S. / Becker, S. / Lange, A.
History
DepositionAug 4, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1May 13, 2015Group: Database references
Revision 1.2Jun 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 1.3May 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

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)8,1921
Polymers8,1921
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 / 1000structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein Ubiquitin


Mass: 8192.375 Da / Num. of mol.: 1 / Fragment: UNP residuse 1-72
Source method: isolated from a genetically manipulated source
Details: UBB / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111PDSD
121PDSD
131NCA
141NCO
151INEPT
161NCACX
171NCOCX
181PDSD
191PDSD
1101PDSD
1111NCA
1121PDSD
1131PDSD
1141PDSD
1151NCA
NMR detailsText: three different labeled samples Ubiquitin-unif [13C-15N] uniformly labeled Ubiquitin-1glc [13C-15N]-1glucose labeled Ubiquitin-2glu [13C-15N]-2glucose labeled

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Sample preparation

DetailsContents: 20 mg [U-100% 13C; U-100% 15N] Ubiquitin, 30 mg [1-glucose 13C,U-100% 15N] Ubiquitin, 40 mg [2-glucose 13C,U-100% 15N] Ubiquitin, 40 % v/v MPD, 0.2 M CdCl2, 1 mg DSS, 100% H20
Solvent system: 100% H20
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mg/mLUbiquitin-1[U-100% 13C; U-100% 15N]1
30 mg/mLUbiquitin-2[1-glucose 13C,U-100% 15N]1
40 mg/mLUbiquitin-3[2-glucose 13C,U-100% 15N]1
40 v/vMPD-41
0.2 mg/mLCdCl2-51
1 mg/mLDSS-61
Sample conditionsPressure: ambient / Temperature: 273 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE8502
Bruker AvanceBrukerAVANCE6003

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.36Bruker Biospinprocessing
X-PLOR NIH2.36Bruker Biospinchemical shift assignment
X-PLOR NIH2.36Bruker Biospindata analysis
X-PLOR NIH2.36Bruker Biospinrefinement
X-PLOR NIH2.36Bruker Biospinstructure validation
X-PLOR NIH2.36Goddardprocessing
X-PLOR NIH2.36Goddardchemical shift assignment
X-PLOR NIH2.36Goddarddata analysis
X-PLOR NIH2.36Goddardrefinement
X-PLOR NIH2.36Goddardstructure validation
X-PLOR NIH2.36Cornilescu, Delaglio and Baxprocessing
X-PLOR NIH2.36Cornilescu, Delaglio and Baxchemical shift assignment
X-PLOR NIH2.36Cornilescu, Delaglio and Baxdata analysis
X-PLOR NIH2.36Cornilescu, Delaglio and Baxrefinement
X-PLOR NIH2.36Cornilescu, Delaglio and Baxstructure validation
X-PLOR NIH2.36Schwieters, Kuszewski, Tjandra and Cloreprocessing
X-PLOR NIH2.36Schwieters, Kuszewski, Tjandra and Clorechemical shift assignment
X-PLOR NIH2.36Schwieters, Kuszewski, Tjandra and Cloredata analysis
X-PLOR NIH2.36Schwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIH2.36Schwieters, Kuszewski, Tjandra and Clorestructure validation
X-PLOR NIH2.36Bhattacharya and Montelioneprocessing
X-PLOR NIH2.36Bhattacharya and Montelionechemical shift assignment
X-PLOR NIH2.36Bhattacharya and Montelionedata analysis
X-PLOR NIH2.36Bhattacharya and Montelionerefinement
X-PLOR NIH2.36Bhattacharya and Montelionestructure validation
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 10

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