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- PDB-6uyj: hRpn13:hRpn2:K48-diubiquitin -

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Basic information

Entry
Database: PDB / ID: 6uyj
TitlehRpn13:hRpn2:K48-diubiquitin
Components
  • (Ubiquitin) x 2
  • 26S proteasome non-ATPase regulatory subunit 1
  • Proteasomal ubiquitin receptor ADRM1
KeywordsPROTEIN BINDING / ubiquitin receptor
Function / homology
Function and homology information


proteasome accessory complex / proteasome regulatory particle / proteasome regulatory particle, lid subcomplex / proteasome regulatory particle, base subcomplex / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / Regulation of ornithine decarboxylase (ODC) / positive regulation of protein monoubiquitination / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) ...proteasome accessory complex / proteasome regulatory particle / proteasome regulatory particle, lid subcomplex / proteasome regulatory particle, base subcomplex / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / Regulation of ornithine decarboxylase (ODC) / positive regulation of protein monoubiquitination / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / fat pad development / mitochondrion transport along microtubule / Somitogenesis / molecular function inhibitor activity / female gonad development / seminiferous tubule development / proteasome binding / regulation of protein catabolic process / male meiosis I / proteasome storage granule / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / endopeptidase activator activity / proteasome assembly / energy homeostasis / regulation of neuron apoptotic process / neuron projection morphogenesis / enzyme regulator activity / regulation of proteasomal protein catabolic process / 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 / 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 / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / 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 / Regulation of FZD by ubiquitination / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / Regulation of innate immune responses to cytosolic DNA / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / VLDLR internalisation and degradation / Regulation of PTEN localization / proteasome complex / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / InlB-mediated entry of Listeria monocytogenes into host cell / Translesion synthesis by POLK / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Josephin domain DUBs / Translesion synthesis by POLI / IKK complex recruitment mediated by RIP1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / Gap-filling DNA repair synthesis and ligation in GG-NER / positive regulation of protein ubiquitination / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / regulation of mitochondrial membrane potential / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / activated TAK1 mediates p38 MAPK activation / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA
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. / : / 26S proteasome subunit RPN2, N-terminal domain / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn2/Psmd1 subunit / 26S proteasome regulatory subunit RPN2, C-terminal / 26S proteasome regulatory subunit RPN2 C-terminal domain / Proteasome/cyclosome repeat / Proteasome/cyclosome repeat / HEAT repeats / PH-domain like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Armadillo-like helical / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Armadillo-type fold / Ubiquitin-like domain superfamily / Roll / Roll / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-B / Proteasomal ubiquitin receptor ADRM1 / 26S proteasome non-ATPase regulatory subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsLu, X. / Walters, K.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)1 ZIA BC011490 United States
CitationJournal: Structure / Year: 2020
Title: An Extended Conformation for K48 Ubiquitin Chains Revealed by the hRpn2:Rpn13:K48-Diubiquitin Structure.
Authors: Lu, X. / Ebelle, D.L. / Matsuo, H. / Walters, K.J.
History
DepositionNov 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 20, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Ubiquitin
D: Ubiquitin
A: Proteasomal ubiquitin receptor ADRM1
B: 26S proteasome non-ATPase regulatory subunit 1


Theoretical massNumber of molelcules
Total (without water)36,3404
Polymers36,3404
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry, chain C and D are linked by covalent bond between C/K48 and D/G76.
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 100structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein Ubiquitin


Mass: 8691.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47
#2: Protein Ubiquitin


Mass: 8604.845 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47
#3: Protein Proteasomal ubiquitin receptor ADRM1 / 110 kDa cell membrane glycoprotein / Gp110 / Adhesion-regulating molecule 1 / ARM-1 / Proteasome ...110 kDa cell membrane glycoprotein / Gp110 / Adhesion-regulating molecule 1 / ARM-1 / Proteasome regulatory particle non-ATPase 13 / hRpn13 / Rpn13 homolog


Mass: 17040.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADRM1, GP110 / Production host: Escherichia coli (E. coli) / References: UniProt: Q16186
#4: Protein/peptide 26S proteasome non-ATPase regulatory subunit 1 / 26S proteasome regulatory subunit RPN2 / 26S proteasome regulatory subunit S1 / 26S proteasome subunit p112


Mass: 2003.036 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99460
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic23D 1H-13C NOESY
122isotropic23D 1H-13C NOESY
131isotropic13D 1H-13C half-filtered NOESY
142isotropic13D 1H-13C half-filtered NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.6 mM [U-13C] Rpn13, 0.6 mM Rpn2, 0.72 mM [U-13C] proximal ubiquitin, 0.72 mM distal ubiquitin, 100% D2OTernary-13C-P100% D2O
solution20.6 mM [U-13C] Rpn13, 0.6 mM Rpn2, 0.72 mM [U-13C] proximal ubiquitin, 0.72 mM distal ubiquitin, 100% D2OTernary-13C-D100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMRpn13[U-13C]1
0.6 mMRpn2natural abundance1
0.72 mMproximal ubiquitin[U-13C]1
0.72 mMdistal ubiquitinnatural abundance1
0.6 mMRpn13[U-13C]2
0.6 mMRpn2natural abundance2
0.72 mMproximal ubiquitin[U-13C]2
0.72 mMdistal ubiquitinnatural abundance2
Sample conditionsIonic strength: 0.11 M / Label: condition_1 / pH: 6.5 / Pressure: ambient atm / Temperature: 298.15 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III8501
Bruker AVANCE IIIBrukerAVANCE III9002

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
XEASYBartels et al.data analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 15

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