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- PDB-1wr1: The complex structure of Dsk2p UBA with ubiquitin -

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Basic information

Entry
Database: PDB / ID: 1wr1
TitleThe complex structure of Dsk2p UBA with ubiquitin
Components
  • Ubiquitin
  • Ubiquitin-like protein DSK2
KeywordsSIGNALING PROTEIN / UBA DOMAIN / UBA-UBIQUITIN COMPLEX / DSK2
Function / homology
Function and homology information


: / : / : / : / : / Regulation of TP53 Degradation / Josephin domain DUBs / Cargo recognition for clathrin-mediated endocytosis / RAS processing / spindle pole body duplication ...: / : / : / : / : / Regulation of TP53 Degradation / Josephin domain DUBs / Cargo recognition for clathrin-mediated endocytosis / RAS processing / spindle pole body duplication / 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 / protein localization to vacuole / 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 / polyubiquitin modification-dependent protein binding / Ub-specific processing proteases / ERAD pathway / ribosomal large subunit assembly / modification-dependent protein catabolic process / protein tag activity / ribosome biogenesis / protein-macromolecule adaptor activity / ubiquitin-dependent protein catabolic process / cytosolic large ribosomal subunit / cytoplasmic translation / protein ubiquitination / structural constituent of ribosome / ubiquitin protein ligase binding / nucleus / cytoplasm / cytosol
Similarity search - Function
: / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / Ubiquitin-associated (UBA) domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Ribosomal L40e family / Ribosomal_L40e ...: / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / Ubiquitin-associated (UBA) domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Helicase, Ruva Protein; domain 3 / 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 / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin / Ubiquitin domain-containing protein DSK2 / Ubiquitin-60S ribosomal protein L40
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing, molecular dynamics, energy minimization
AuthorsOhno, A. / Jee, J.G. / Fujiwara, K. / Tenno, T. / Goda, N. / Tochio, H. / Hiroaki, H. / kobayashi, H. / Shirakawa, M.
CitationJournal: Structure / Year: 2005
Title: Structure of the UBA domain of Dsk2p in complex with ubiquitin molecular determinants for ubiquitin recognition.
Authors: Ohno, A. / Jee, J. / Fujiwara, K. / Tenno, T. / Goda, N. / Tochio, H. / Kobayashi, H. / Hiroaki, H. / Shirakawa, M.
History
DepositionOct 8, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 9, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: pdbx_nmr_software / pdbx_struct_assembly ...pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct / struct_ref_seq_dif
Item: _pdbx_nmr_software.name / _struct.title / _struct_ref_seq_dif.details
Revision 1.4Sep 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn / diffrn_radiation / diffrn_radiation_wavelength
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin
B: Ubiquitin-like protein DSK2


Theoretical massNumber of molelcules
Total (without water)14,7512
Polymers14,7512
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area840 Å2
ΔGint-4 kcal/mol
Surface area8010 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #16closest to the average

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Components

#1: Protein Ubiquitin


Mass: 8568.769 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: UBI4 (1224-1451) / Plasmid: pET-24a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P61864, UniProt: P0CG63*PLUS
#2: Protein Ubiquitin-like protein DSK2


Mass: 6181.740 Da / Num. of mol.: 1 / Fragment: C-TERMINAL UBA DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: DSK2 (982-1120) / Plasmid: pGEX-KG / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P48510

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1114D 13C/15N-separated NOESY
1213D 15N-separated NOESY
1313D 13C-separated NOESY
1413D 13C-edited/13C-filtered-NOESY
1524D 13C/15N-separated NOESY
1623D 15N-separated NOESY
1723D 13C-separated ROESY
1823D 13C-edited/13C-filtered-NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
1U-15N, 13C ubiquitin + DSK2-UBA complex (0.9mM)20mM Phosphate buffer (pH 6.8); 5mM potassium chloride; 1mM EDTA; 5% D2O
2U-15N, 13C DSK2-UBA + ubiquitin complex (1.0mM)20mM Phosphate buffer (pH 6.8); 5mM potassium chloride; 1mM EDTA; 5% D2O
Sample conditionsIonic strength: 20mM potassium phosphate, 5mM potassium chloride
pH: 6.8 / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Varian INOVAVarianINOVA9002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5collection
VNMR6.1Ccollection
NMRPipe2.1Delaglioprocessing
Sparky3.1.0.0Goddarddata analysis
CYANA2.0.17Guntertstructure solution
Amber7Pearlmanrefinement
RefinementMethod: torsion angle dynamics, simulated annealing, molecular dynamics, energy minimization
Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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