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- PDB-1otr: Solution Structure of a CUE-Ubiquitin Complex -

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Basic information

Entry
Database: PDB / ID: 1otr
TitleSolution Structure of a CUE-Ubiquitin Complex
Components
  • Ubiquitin
  • protein Cue2
KeywordsCELL CYCLE / PROTEIN-PROTEIN COMPLEX
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 / PINK1-PRKN Mediated Mitophagy / Pexophagy / Interleukin-1 signaling / Aggrephagy / Regulation of pyruvate metabolism / nuclear-transcribed mRNA catabolic process, no-go decay / 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 REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Translesion Synthesis by POLH / 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 / K63-linked polyubiquitin modification-dependent protein binding / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / CDK-mediated phosphorylation and removal of Cdc6 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Major pathway of rRNA processing in the nucleolus and cytosol / KEAP1-NFE2L2 pathway / Neddylation / Formation of TC-NER Pre-Incision Complex / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / Gap-filling DNA repair synthesis and ligation in TC-NER / Antigen processing: Ubiquitination & Proteasome degradation / L13a-mediated translational silencing of Ceruloplasmin expression / polyubiquitin modification-dependent protein binding / Dual incision in TC-NER / ribosomal large subunit export from nucleus / Ub-specific processing proteases / cytosolic ribosome / RNA endonuclease activity / rescue of stalled ribosome / ubiquitin binding / modification-dependent protein catabolic process / protein tag activity / peroxisome / ribosome biogenesis / ribosomal large subunit assembly / cytoplasmic translation / endonuclease activity / cytosolic large ribosomal subunit / protein ubiquitination / structural constituent of ribosome / ubiquitin protein ligase binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ubiquitin-binding protein Cue2, CUE domain 1 / Ubiquitin-binding protein Cue2, CUE domain 2 / : / Small MutS-related domain / Smr domain superfamily / Smr domain / Smr domain profile. / CUE domain / Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs) / Ubiquitin system component CUE ...Ubiquitin-binding protein Cue2, CUE domain 1 / Ubiquitin-binding protein Cue2, CUE domain 2 / : / Small MutS-related domain / Smr domain superfamily / Smr domain / Smr domain profile. / CUE domain / Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs) / Ubiquitin system component CUE / CUE domain profile. / Ubiquitin-associated (UBA) domain / 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 / Endonuclease CUE2 / Ubiquitin-60S ribosomal protein L40
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
AuthorsKang, R.S. / Daniels, C.M. / Salerno, W.J. / Radhakrishnan, I.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2003
Title: Solution Structure of a CUE-Ubiquitin Complex Reveals a Conserved Mode of Ubiquitin Binding
Authors: Kang, R.S. / Daniels, C.M. / Francis, S.A. / Shih, S.C. / Salerno, W.J. / Hicke, L. / Radhakrishnan, I.
History
DepositionMar 22, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: protein Cue2
B: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)14,1422
Polymers14,1422
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 / 80The submitted conformer models are the 20 structures with the lowest restraint energies, restraint violations, and RMS deviations from ideal covalent geometry
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide protein Cue2 / HYPOTHETICAL 50.9 KD PROTEIN IN BUD2-MIF2 INTERGENIC REGION / hypothetical protein YKL090w


Mass: 5573.291 Da / Num. of mol.: 1 / Fragment: Amino-terminal CUE Domain, Residues 6-54
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CUE2 / Plasmid: pMCSG / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P36075
#2: 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: UBI1 / Plasmid: pET-3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / 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
1113D 15N-separated NOESY
1223D 13C-separated NOESY
1333D 13C-filtered, 13C-edited NOESY
1442D DOUBLE HALF-FILTERED NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM U-15N,13C Cue2 + 1 mM Ubiquitin; 20 mM sodium phosphate buffer, pH 7.0, 0.2% NaN390% H2O/10% D2O
21 mM U-15N,13C Cue2 + 1 mM Ubiquitin; 20 mM sodium phosphate buffer, pH 7.0, 0.2% NaN399.996% D2O
31 mM Cue2 + 1 mM U-15N,13C Ubiquitin; 20 mM sodium phosphate buffer, pH 7.0, 0.2% NaN390% H2O/10% D2O
41 mM Cue2 + 1 mM U-15N,13C Ubiquitin; 20 mM sodium phosphate buffer, pH 7.0, 0.2% NaN399.996% D2O
Sample conditionsIonic strength: 20 mM sodium phosphate, pH 7.0, 0.2% NaN3 / pH: 7 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1bVariancollection
Felix98.0 and 2000Accelrysprocessing
Felix98.0 and 2000Accelrysdata analysis
CNS1.1Brunger et al.structure solution
ARIA1.2Linge and Nilgesstructure solution
ARIA1.2Linge and Nilgesrefinement
CNS1.1Brunger et al.refinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 3328 distance restraints, including 3238 NOE-derived distance restraints [2560 unambiguous and 678 ambiguous restraints], 90 hydrogen bonding distance ...Details: The structures are based on a total of 3328 distance restraints, including 3238 NOE-derived distance restraints [2560 unambiguous and 678 ambiguous restraints], 90 hydrogen bonding distance restraints, and 150 torsion angle restraints.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: The submitted conformer models are the 20 structures with the lowest restraint energies, restraint violations, and RMS deviations from ideal covalent geometry
Conformers calculated total number: 80 / Conformers submitted total number: 20

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