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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


Degradation of CRY and PER proteins / Degradation of CDH1 / Regulation of ornithine decarboxylase (ODC) / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA ...Degradation of CRY and PER proteins / Degradation of CDH1 / Regulation of ornithine decarboxylase (ODC) / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / SCF(Skp2)-mediated degradation of p27/p21 / Assembly of the pre-replicative complex / CDK-mediated phosphorylation and removal of Cdc6 / Autodegradation of the E3 ubiquitin ligase COP1 / G2/M Checkpoints / Degradation of AXIN / Asymmetric localization of PCP proteins / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Regulation of RUNX3 expression and activity / Regulation of RAS by GAPs / Regulation of PTEN stability and activity / follicle-stimulating hormone signaling pathway / Regulation of RUNX2 expression and activity / Degradation of GLI1 by the proteasome / UCH proteinases / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Degradation of DVL / Orc1 removal from chromatin / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Dectin-1 mediated noncanonical NF-kB signaling / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / Hedgehog ligand biogenesis / Hedgehog 'on' state / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Degradation of beta-catenin by the destruction complex / : / : / Activation of NF-kappaB in B cells / protein modification process => GO:0036211 / The role of GTSE1 in G2/M progression after G2 checkpoint / FCERI mediated NF-kB activation / CLEC7A (Dectin-1) signaling / Interleukin-1 signaling / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Downstream TCR signaling / Separation of Sister Chromatids / MAPK6/MAPK4 signaling / Sertoli cell development / GLI3 is processed to GLI3R by the proteasome / ABC-family proteins mediated transport / positive regulation of growth hormone receptor signaling pathway / Neddylation / Ub-specific processing proteases / KEAP1-NFE2L2 pathway / regulation of T cell differentiation in thymus / Antigen processing: Ubiquitination & Proteasome degradation / proteasome regulatory particle, lid subcomplex / molecular function inhibitor activity / oogenesis / seminiferous tubule development / proteasome binding / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / spermatid development / Eukaryotic Translation Termination / adipose tissue development / SRP-dependent cotranslational protein targeting to membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / Viral mRNA Translation / endopeptidase activator activity / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / proteasome assembly / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / ovarian follicle development / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / : / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex / Prevention of phagosomal-lysosomal fusion / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation
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-like (UB roll) / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Roll / Ubiquitin-like domain superfamily / 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
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Water00
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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