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- PDB-2jwz: Mutations in the hydrophobic core of ubiquitin differentially aff... -

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Basic information

Entry
Database: PDB / ID: 2jwz
TitleMutations in the hydrophobic core of ubiquitin differentially affect its recognition by receptor proteins
ComponentsUbiquitin
KeywordsSIGNALING PROTEIN / UBIQUITIN / L69S MUTANT / CORE MUTATION / Cytoplasm / DNA damage / DNA repair / Nucleus / Phosphorylation / Ubl conjugation / PROTEASOMAL DEGRADATION
Function / homology
Function and homology information


: / : / : / : / : / Regulation of TP53 Degradation / Josephin domain DUBs / RAS processing / Regulation of PTEN localization / ER Quality Control Compartment (ERQC) ...: / : / : / : / : / Regulation of TP53 Degradation / Josephin domain DUBs / RAS processing / Regulation of PTEN localization / ER Quality Control Compartment (ERQC) / UCH proteinases / Pexophagy / Interleukin-1 signaling / Aggrephagy / Peroxisomal protein import / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / ABC-family proteins mediated transport / Metalloprotease DUBs / Endosomal Sorting Complex Required For Transport (ESCRT) / E3 ubiquitin ligases ubiquitinate target proteins / Translesion Synthesis by POLH / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Termination of translesion DNA synthesis / Negative regulators of DDX58/IFIH1 signaling / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / KEAP1-NFE2L2 pathway / CDK-mediated phosphorylation and removal of Cdc6 / Neddylation / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Formation of TC-NER Pre-Incision Complex / Major pathway of rRNA processing in the nucleolus and cytosol / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Gap-filling DNA repair synthesis and ligation in TC-NER / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Antigen processing: Ubiquitination & Proteasome degradation / L13a-mediated translational silencing of Ceruloplasmin expression / Dual incision in TC-NER / ribosomal large subunit export from nucleus / Ub-specific processing proteases / ribosomal large subunit assembly / modification-dependent protein catabolic process / protein tag activity / ribosome biogenesis / cytosolic large ribosomal subunit / cytoplasmic translation / protein ubiquitination / structural constituent of ribosome / ubiquitin protein ligase binding / nucleus / cytoplasm / cytosol
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) / Ubiquitin family ...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 / Ubiquitin-60S ribosomal protein L40
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsHaririnia, A. / Verma, R. / Purohit, N. / Twarog, M. / Deshaies, R. / Bolon, D. / Fushman, D.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Mutations in the hydrophobic core of ubiquitin differentially affect its recognition by receptor proteins.
Authors: Haririnia, A. / Verma, R. / Purohit, N. / Twarog, M.Z. / Deshaies, R.J. / Bolon, D. / Fushman, D.
History
DepositionOct 31, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)8,5431
Polymers8,5431
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 75structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Ubiquitin


Mass: 8542.688 Da / Num. of mol.: 1 / Mutation: L69S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: UBI1, RPL40A / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 DE3(PLYSS) / References: UniProt: P61864, UniProt: P0CG63*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-1H TOCSY
1312D 1H-1H NOESY
1413D 15N-SEPARATED TOCSY
1512D 1H-15N IPAP
161HMQC-J
17115N R1 AND R2
18115N{1H} NOE
NMR detailsText: RESIDUAL DIPOLAR COUPLINGS WERE MEASURED IN POLYETHYLENE GLYCOL BASED ALIGNMENT MEDIUM

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Sample preparation

DetailsContents: 2 mM [U-100% 15N] L69S UBIQUITIN, 2 mM L69S UBIQUITIN, 93% H2O/7% D2O
Solvent system: 93% H2O/7% D2O
SampleConc.: 2 mM / Component: L69S UBIQUITIN / Isotopic labeling: [U-100% 15N]
Sample conditionsIonic strength: 20 mM / pH: 6.8 / Pressure: AMBIENT / Temperature: 296 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
ARIA2Linge, O'Donoghue and Nilgesstructure solution
ARIA2Linge, O'Donoghue and Nilgesrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 75 / Conformers submitted total number: 10

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