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- PDB-5ymy: The structure of the complex between Rpn13 and K48-diUb -

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Basic information

Entry
Database: PDB / ID: 5ymy
TitleThe structure of the complex between Rpn13 and K48-diUb
Components
  • (Ubiquitin) x 2
  • Proteasomal ubiquitin receptor ADRM1
KeywordsPROTEIN BINDING/SIGNALING PROTEIN / complex / ubiquitin receptor / compacted / PROTEIN BINDING-SIGNALING PROTEIN complex
Function / homology
Function and homology information


proteasome regulatory particle, lid 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 ...proteasome regulatory particle, lid 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 / male meiosis I / 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 / 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 / proteasome complex / VLDLR internalisation and degradation / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / 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 / Regulation of activated PAK-2p34 by proteasome mediated degradation / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / 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 / regulation of mitochondrial membrane potential / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / activated TAK1 mediates p38 MAPK activation / 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 / Regulation of signaling by CBL / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Assembly of the pre-replicative complex
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 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Roll / Ubiquitin-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
Polyubiquitin-B / Proteasomal ubiquitin receptor ADRM1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsLiu, Z. / Dong, X. / Gong, Z. / Yi, H.W. / Liu, K. / Yang, J. / Zhang, W.P. / Tang, C.
Funding support China, 7items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2016YFA0501200 China
National Basic Research Program of China (973 Program)2013CB910200 China
National Natural Science Foundation of China31770799 China
National Natural Science Foundation of China81573400 China
National Natural Science Foundation of China31500595 China
National Natural Science Foundation of China31400735 China
National Natural Science Foundation of China31400644 China
CitationJournal: Cell Discov / Year: 2019
Title: Structural basis for the recognition of K48-linked Ub chain by proteasomal receptor Rpn13.
Authors: Liu, Z. / Dong, X. / Yi, H.W. / Yang, J. / Gong, Z. / Wang, Y. / Liu, K. / Zhang, W.P. / Tang, C.
History
DepositionOct 22, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references / Category: citation / pdbx_database_related
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI
Revision 1.2Apr 24, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Nov 13, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin
B: Ubiquitin
C: Proteasomal ubiquitin receptor ADRM1


Theoretical massNumber of molelcules
Total (without water)33,9243
Polymers33,9243
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area3250 Å2
ΔGint-6 kcal/mol
Surface area13420 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 240structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: 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: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47
#2: Protein Ubiquitin


Mass: 8604.845 Da / Num. of mol.: 1 / Mutation: K48R
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: 16742.045 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
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
111isotropic22D 1H-15N HSQC
121isotropic13D HNCA
131isotropic13D HNCB
141isotropic13D (H)CCH-TOCSY
152isotropic1filter NOESY
NMR detailsText: The author states that they used conjoined torsion angle/rigid body simulated annealing refinement based on 19 inter-molecular NOEs (deposited in this entry), the Rpn13 structure from PDB ID ...Text: The author states that they used conjoined torsion angle/rigid body simulated annealing refinement based on 19 inter-molecular NOEs (deposited in this entry), the Rpn13 structure from PDB ID 2R2Y, and the Ub structure from 1UBQ.

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Sample preparation

DetailsType: solution
Contents: 0.58 mM [U-13C; U-15N; U-2H] Rpn13, 20 mM MES, 0.15 M sodium chloride, 90% H2O/10% D2O
Label: rpn13 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.58 mMRpn13[U-13C; U-15N; U-2H]1
20 mMMESnatural abundance1
0.15 Msodium chloridenatural abundance1
Sample conditionsIonic strength: 150 mM / Label: ass / pH: 6.5 / Pressure: 760 mmHg / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III8501
Bruker AVANCE IIIBrukerAVANCE III6002

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
AnalysisCCPNchemical shift assignment
AnalysisCCPNpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 240 / Conformers submitted total number: 20

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