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- PDB-2z59: Complex Structures of Mouse Rpn13 (22-130aa) and ubiquitin -

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Basic information

Entry
Database: PDB / ID: 2z59
TitleComplex Structures of Mouse Rpn13 (22-130aa) and ubiquitin
Components
  • Protein ADRM1
  • Ubiquitin
KeywordsPROTEIN TRANSPORT / Proteasome / PH domain
Function / homology
Function and homology information


follicle-stimulating hormone signaling pathway / UCH proteinases / : / : / Sertoli cell development / protein modification process => GO:0036211 / positive regulation of growth hormone receptor signaling pathway / Ub-specific processing proteases / proteasome regulatory particle, lid subcomplex / regulation of T cell differentiation in thymus ...follicle-stimulating hormone signaling pathway / UCH proteinases / : / : / Sertoli cell development / protein modification process => GO:0036211 / positive regulation of growth hormone receptor signaling pathway / Ub-specific processing proteases / proteasome regulatory particle, lid subcomplex / regulation of T cell differentiation in thymus / oogenesis / proteasome binding / molecular function inhibitor activity / seminiferous tubule development / spermatid development / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / endopeptidase activator activity / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / proteasome assembly / adipose tissue development / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / ovarian follicle development / 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 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Endosomal Sorting Complex Required For Transport (ESCRT) / NOTCH2 Activation and Transmission of Signal to the Nucleus / 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 / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / InlA-mediated entry of Listeria monocytogenes into host cells / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / Translesion synthesis by REV1 / NF-kB is activated and signals survival / Regulation of PTEN localization / Translesion synthesis by POLK / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / proteasome complex / Translesion synthesis by POLI / cytosolic ribosome / Gap-filling DNA repair synthesis and ligation in GG-NER / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / 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) / thymus development / 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 / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / Regulation of NF-kappa B signaling / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / Negative regulators of DDX58/IFIH1 signaling / TNFR2 non-canonical NF-kB pathway
Similarity search - Function
Proteasomal ubiquitin receptor Rpn13/ADRM1 / RPN13, DEUBAD domain / RPN13, DEUBAD domain superfamily / UCH-binding domain / DEUBAD domain / DEUBAD (DEUBiquitinase ADaptor) domain profile. / Proteasomal ubiquitin receptor Rpn13/ADRM1 / Proteasomal ubiquitin receptor Rpn13/ADRM1, Pru domain superfamily / Rpn13/ADRM1, Pru domain / Proteasome complex subunit Rpn13, Pru domain ...Proteasomal ubiquitin receptor Rpn13/ADRM1 / RPN13, DEUBAD domain / RPN13, DEUBAD domain superfamily / UCH-binding domain / DEUBAD domain / DEUBAD (DEUBiquitinase ADaptor) domain profile. / Proteasomal ubiquitin receptor Rpn13/ADRM1 / Proteasomal ubiquitin receptor Rpn13/ADRM1, Pru domain superfamily / Rpn13/ADRM1, Pru domain / Proteasome complex subunit Rpn13, Pru domain / Pru (pleckstrin-like receptor for ubiquitin) domain profile. / PH-domain like / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Roll / Roll / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-C / Ubiquitin-60S ribosomal protein L40 / Proteasomal ubiquitin receptor ADRM1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodSOLUTION NMR / High Ambiguity Driven protein-protein DOCKing
AuthorsChen, X. / Schreiner, P. / Groll, M. / Walters, K.J.
CitationJournal: Nature / Year: 2008
Title: Ubiquitin docking at the proteasome through a novel pleckstrin-homology domain interaction.
Authors: Schreiner, P. / Chen, X. / Husnjak, K. / Randles, L. / Zhang, N. / Elsasser, S. / Finley, D. / Dikic, I. / Walters, K.J. / Groll, M.
History
DepositionJul 1, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 20, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
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: Protein ADRM1
B: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)21,3642
Polymers21,3642
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Protein ADRM1 / Proteasome Component Rpn13 / Adhesion-regulating molecule 1 / 110 kDa cell membrane glycoprotein / ...Proteasome Component Rpn13 / Adhesion-regulating molecule 1 / 110 kDa cell membrane glycoprotein / Gp110 / ARM-1


Mass: 12787.631 Da / Num. of mol.: 1 / Fragment: residues 22-130
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Adrm1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q9JKV1
#2: Protein Ubiquitin /


Mass: 8576.831 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Rps27a, Uba80, Ubcep1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62988, UniProt: P0CG48*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HN(CA)CB, HNCA/HN(CO)CA
1223D 15N-separated NOESY
1333D 15N-separated NOESY
144HSQC titration
155HSQC titration
166HSQC titration

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6mM MmRpn13 U-15N, 13C; U-70% 2H; 20mM phosphate buffer; 30mM NaCl; 3mM DTT; 90% H2O, 10% D2O90% H2O/10% D2O
20.6mM MmRpn13 U-15N; U-50% 2H; 20mM phosphate buffer; 30mM NaCl; 3mM DTT; 90% H2O, 10% D2O90% H2O/10% D2O
30.6mM MmRpn13 U-15N, 13C; U-70% 2H; 0.6mM ubiquitin; 20mM phosphate buffer; 30mM NaCl; 3mM DTT; 90% H2O, 10% D2O90% H2O/10% D2O
40.4mM MmRpn13 U-15N; 20mM phosphate buffer; 30mM NaCl; 3mM DTT; 90% H2O, 10% D2O90% H2O/10% D2O
50.4mM ubiquitin U-15N; 20mM phosphate buffer; 30mM NaCl; 3mM DTT; 90% H2O, 10% D2O90% H2O/10% D2O
60.4mM MmRpn13 U-13C; 20mM phosphate buffer; 30mM NaCl; 3mM DTT; 100% D2O100% D2O
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2006Frank Delaglio, Stephan Grzesiek, Guang Zhu, Geerten W. Vuister, John Pfeifer and Ad Baxprocessing
XEASY1996Tai-he Xia and Christian Bartelsdata analysis
HADDOCK1.3Cyril Dominguez, Rolf Boelens, Alexandre M.J.J.Bonvinstructure solution
HADDOCK1.3Cyril Dominguez, Rolf Boelens, Alexandre M.J.J.Bonvinrefinement
RefinementMethod: High Ambiguity Driven protein-protein DOCKing / Software ordinal: 1
Details: The strctures are based on interaction data such as chemical shift perturbation data resulting from NMR titration experiments and intermolecular NOE.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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