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Open data
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Basic information
Entry | Database: PDB / ID: 1otr | ||||||
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Title | Solution Structure of a CUE-Ubiquitin Complex | ||||||
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![]() | CELL CYCLE / PROTEIN-PROTEIN COMPLEX | ||||||
Function / homology | ![]() : / : / : / : / : / : / Regulation of TP53 Degradation / Josephin domain DUBs / RAS processing / Regulation of PTEN localization ...: / : / : / : / : / : / 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 / 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 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 / ubiquitin binding / ribosomal large subunit assembly / modification-dependent protein catabolic process / protein tag activity / ribosome biogenesis / endonuclease activity / cytosolic large ribosomal subunit / cytoplasmic translation / protein ubiquitination / structural constituent of ribosome / ubiquitin protein ligase binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | SOLUTION NMR / torsion angle dynamics, simulated annealing | ||||||
![]() | Kang, R.S. / Daniels, C.M. / Salerno, W.J. / Radhakrishnan, I. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 774.1 KB | Display | ![]() |
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PDB format | ![]() | 650.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 351.8 KB | Display | ![]() |
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Full document | ![]() | 613 KB | Display | |
Data in XML | ![]() | 49.4 KB | Display | |
Data in CIF | ![]() | 70.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: Protein/peptide | 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.) ![]() ![]() Gene: CUE2 / Plasmid: pMCSG / Species (production host): Escherichia coli / Production host: ![]() ![]() |
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#2: Protein | Mass: 8568.769 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: UBI1 / Plasmid: pET-3a / Species (production host): Escherichia coli / Production host: ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
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NMR experiment |
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Sample preparation
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Sample conditions | Ionic strength: 20 mM sodium phosphate, pH 7.0, 0.2% NaN3 / pH: 7.0 / Pressure: 1 atm / Temperature: 298 K | |||||||||||||||
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz |
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Processing
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Refinement | Method: 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 representative | Selection criteria: closest to the average | ||||||||||||||||||||||||||||||||
NMR ensemble | Conformer 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 |