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- PDB-2n3u: Solution structure of the Rpn1 T1 site engaging two monoubiquitin... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2n3u | ||||||
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Title | Solution structure of the Rpn1 T1 site engaging two monoubiquitin molecules | ||||||
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![]() | PROTEIN BINDING | ||||||
Function / homology | ![]() proteasome regulatory particle, base subcomplex / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / 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 / regulation of protein catabolic process ...proteasome regulatory particle, base subcomplex / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / 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 / regulation of protein catabolic process / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / Peptide chain elongation / proteasome storage granule / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Antigen processing: Ubiquitination & Proteasome degradation / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Viral mRNA Translation / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Ub-specific processing proteases / cytosolic ribosome / enzyme regulator activity / 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 / 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 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / Neutrophil degranulation / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / 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 / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / proteasome complex / 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 / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / TCF dependent signaling in response to WNT / AUF1 (hnRNP D0) binds and destabilizes mRNA / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
![]() | Chen, X. / Walters, K.J. | ||||||
![]() | ![]() Title: Rpn1 provides adjacent receptor sites for substrate binding and deubiquitination by the proteasome. Authors: Shi, Y. / Chen, X. / Elsasser, S. / Stocks, B.B. / Tian, G. / Lee, B.H. / Shi, Y. / Zhang, N. / de Poot, S.A. / Tuebing, F. / Sun, S. / Vannoy, J. / Tarasov, S.G. / Engen, J.R. / Finley, D. / Walters, K.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 859.5 KB | Display | ![]() |
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PDB format | ![]() | 712.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 562.7 KB | Display | ![]() |
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Full document | ![]() | 867.6 KB | Display | |
Data in XML | ![]() | 77.1 KB | Display | |
Data in CIF | ![]() | 94 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2n3tC ![]() 2n3vC ![]() 2n3wC C: citing same article ( |
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Similar structure data | |
Other databases |
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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 | Mass: 13636.592 Da / Num. of mol.: 1 / Fragment: UNP residues 482-612 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: RPN1, HRD2, NAS1, RPD1, YHR027C / Plasmid: Pgex4t1 / Production host: ![]() ![]() |
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#2: Protein | Mass: 8576.831 Da / Num. of mol.: 2 / Fragment: UNP residues 1-76 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-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: 50 / pH: 6.7 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 850 MHz |
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Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | |||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | |||||||||||||||||||||||||||
NMR ensemble | Conformers calculated total number: 50 / Conformers submitted total number: 10 |