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- PDB-7kxi: Structure of XL5-ligated hRpn13 Pru domain -

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Basic information

Entry
Database: PDB / ID: 7kxi
TitleStructure of XL5-ligated hRpn13 Pru domain
ComponentsProteasomal ubiquitin receptor ADRM1
KeywordsPROTEIN BINDING / Complex
Function / homology
Function and homology information


proteasome regulatory particle, lid subcomplex / Regulation of ornithine decarboxylase (ODC) / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / molecular function inhibitor activity / proteasome binding / endopeptidase activator activity / proteasome assembly / Regulation of activated PAK-2p34 by proteasome mediated degradation ...proteasome regulatory particle, lid subcomplex / Regulation of ornithine decarboxylase (ODC) / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / molecular function inhibitor activity / proteasome binding / endopeptidase activator activity / proteasome assembly / Regulation of activated PAK-2p34 by proteasome mediated degradation / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / proteasome complex / NIK-->noncanonical NF-kB signaling / SCF-beta-TrCP mediated degradation of Emi1 / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / Degradation of AXIN / Hh mutants are degraded by ERAD / Activation of NF-kappaB in B cells / Degradation of GLI1 by the proteasome / Hedgehog ligand biogenesis / G2/M Checkpoints / Defective CFTR causes cystic fibrosis / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Autodegradation of the E3 ubiquitin ligase COP1 / Negative regulation of NOTCH4 signaling / Vif-mediated degradation of APOBEC3G / Regulation of RUNX3 expression and activity / Hedgehog 'on' state / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / MAPK6/MAPK4 signaling / Degradation of beta-catenin by the destruction complex / transcription elongation by RNA polymerase II / ABC-family proteins mediated transport / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / CDK-mediated phosphorylation and removal of Cdc6 / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / Regulation of expression of SLITs and ROBOs / FCERI mediated NF-kB activation / Regulation of PTEN stability and activity / Interleukin-1 signaling / Orc1 removal from chromatin / Regulation of RAS by GAPs / Regulation of RUNX2 expression and activity / The role of GTSE1 in G2/M progression after G2 checkpoint / Separation of Sister Chromatids / KEAP1-NFE2L2 pathway / UCH proteinases / Downstream TCR signaling / Antigen processing: Ubiquitination & Proteasome degradation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / ER-Phagosome pathway / protease binding / proteasome-mediated ubiquitin-dependent protein catabolic process / Ub-specific processing proteases / nucleoplasm / plasma membrane / cytosol
Similarity search - Function
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.
Similarity search - Domain/homology
Chem-XAY / Proteasomal ubiquitin receptor ADRM1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsLu, X. / Walters, K.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)1 ZIA BC011490 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)1 ZIA BC011627 United States
CitationJournal: Nat Commun / Year: 2021
Title: Structure-guided bifunctional molecules hit a DEUBAD-lacking hRpn13 species upregulated in multiple myeloma.
Authors: Lu, X. / Sabbasani, V.R. / Osei-Amponsa, V. / Evans, C.N. / King, J.C. / Tarasov, S.G. / Dyba, M. / Das, S. / Chan, K.C. / Schwieters, C.D. / Choudhari, S. / Fromont, C. / Zhao, Y. / Tran, B. ...Authors: Lu, X. / Sabbasani, V.R. / Osei-Amponsa, V. / Evans, C.N. / King, J.C. / Tarasov, S.G. / Dyba, M. / Das, S. / Chan, K.C. / Schwieters, C.D. / Choudhari, S. / Fromont, C. / Zhao, Y. / Tran, B. / Chen, X. / Matsuo, H. / Andresson, T. / Chari, R. / Swenson, R.E. / Tarasova, N.I. / Walters, K.J.
History
DepositionDec 3, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 29, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Proteasomal ubiquitin receptor ADRM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4682
Polymers17,0401
Non-polymers4271
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: 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
#2: Chemical ChemComp-XAY / 2-{[(2S)-2-cyano-3-{3-[(4-methylbenzene-1-carbonyl)amino]phenyl}propanoyl]amino}benzoic acid


Mass: 427.452 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H21N3O4
Has ligand of interestN
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
212isotropic33D 1H-13C NOESY
226isotropic33D 1H-15N NOESY
233isotropic33D 1H-13C half-filtered NOESY
244isotropic32D 1H-13C half-filtered NOESY
255isotropic33D 1H-13C half-filtered NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution20.4 mM [U-13C] 13C_protein, 0.48 mM ligand, 20% H2O/70% D2O/10% DMSOsample-120% H2O/70% D2O/10% DMSO
solution30.25 mM [U-13C] 13C_protein, 0.5 mM ligand, 90% H2O/10% DMSOsample-290% H2O/10% DMSO
solution40.5 mM protein, 0.5 mM [U-13C] ligand, 90% H2O/10% DMSOsample-390% H2O/10% DMSO
solution50.4 mM protein, 0.4 mM [U-13C] ligand, 20% H2O/70% D2O/10% DMSOsample-420% H2O/70% D2O/10% DMSO
solution60.25 mM [U-15N] protein, 0.5 mM ligand, 90% H2O/10% DMSOsample-590% H2O/10% DMSO
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mM13C_protein[U-13C]2
0.48 mMligandnatural abundance2
0.25 mM13C_protein[U-13C]3
0.5 mMligandnatural abundance3
0.5 mMproteinnatural abundance4
0.5 mMligand[U-13C]4
0.4 mMproteinnatural abundance5
0.4 mMligand[U-13C]5
0.25 mMprotein[U-15N]6
0.5 mMligandnatural abundance6
Sample conditionsIonic strength: 0.11 M / Label: conditions_1 / pH: 6.5 / Pressure: ambient atm / Temperature: 283.15 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 850 MHz

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
XEASYBartels et al.chemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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