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- PDB-6oi4: RPN13 (19-132)-RPN2 (940-952) pY950-Ub complex -

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Basic information

Entry
Database: PDB / ID: 6oi4
TitleRPN13 (19-132)-RPN2 (940-952) pY950-Ub complex
Components
  • 26S proteasome non-ATPase regulatory subunit 1
  • Proteasomal ubiquitin receptor ADRM1
  • ubiquitin
KeywordsPROTEIN BINDING / PRU / proteasome / ubiquitin
Function / homology
Function and homology information


proteasome accessory complex / proteasome regulatory particle / proteasome regulatory particle, lid subcomplex / proteasome regulatory particle, base subcomplex / Regulation of ornithine decarboxylase (ODC) / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / molecular function inhibitor activity / proteasome binding / regulation of protein catabolic process ...proteasome accessory complex / proteasome regulatory particle / proteasome regulatory particle, lid subcomplex / proteasome regulatory particle, base subcomplex / Regulation of ornithine decarboxylase (ODC) / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / molecular function inhibitor activity / proteasome binding / regulation of protein catabolic process / proteasome storage granule / endopeptidase activator activity / proteasome assembly / enzyme regulator activity / 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 / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / 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 / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / NF-kB is activated and signals survival / Regulation of PTEN localization / Regulation of BACH1 activity / Translesion synthesis by REV1 / proteasome complex / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / 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) / 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 / NIK-->noncanonical NF-kB signaling / Regulation of NF-kappa B signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / NOTCH3 Activation and Transmission of Signal to the Nucleus / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Negative regulators of DDX58/IFIH1 signaling / Degradation of DVL / Deactivation of the beta-catenin transactivating complex / transcription elongation by RNA polymerase II / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Hh mutants are degraded by ERAD / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Recognition of DNA damage by PCNA-containing replication complex / Fanconi Anemia Pathway / Negative regulation of FGFR3 signaling / Peroxisomal protein import / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Defective CFTR causes cystic fibrosis
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 / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Armadillo-like helical / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Armadillo-type fold / Ubiquitin-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Polyubiquitin-C / Proteasomal ubiquitin receptor ADRM1 / 26S proteasome non-ATPase regulatory subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsHemmis, C.W. / Hill, C.P.
Funding support United States, 2items
OrganizationGrant numberCountry
American Cancer SocietyPF-16-100-01 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Phosphorylation of Tyr-950 in the proteasome scaffolding protein RPN2 modulates its interaction with the ubiquitin receptor RPN13.
Authors: Hemmis, C.W. / Heard, S.C. / Hill, C.P.
History
DepositionApr 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)47,84215
Polymers47,2846
Non-polymers5599
Water4,468248
1
A: Proteasomal ubiquitin receptor ADRM1
C: ubiquitin
E: 26S proteasome non-ATPase regulatory subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0149
Polymers23,6423
Non-polymers3726
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Proteasomal ubiquitin receptor ADRM1
D: ubiquitin
F: 26S proteasome non-ATPase regulatory subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8286
Polymers23,6423
Non-polymers1863
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.373, 99.373, 41.705
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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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: 13298.175 Da / Num. of mol.: 2 / Fragment: UNP residues 20-132
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADRM1, GP110 / Plasmid: pET151 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) RIL / References: UniProt: Q16186
#2: Protein ubiquitin /


Mass: 8576.831 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG48
#3: Protein/peptide 26S proteasome non-ATPase regulatory subunit 1 / 26S proteasome regulatory subunit RPN2 / 26S proteasome regulatory subunit S1 / 26S proteasome ...26S proteasome regulatory subunit RPN2 / 26S proteasome regulatory subunit S1 / 26S proteasome subunit p112 / RPN2


Mass: 1766.745 Da / Num. of mol.: 2 / Fragment: UNP residues 940-952
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
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 51.08 % / Description: elongated needles
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.8 / Details: 0.1 M citric acid, pH 4.6, 20% PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.76→40 Å / Num. obs: 46327 / % possible obs: 99 % / Redundancy: 9.2 % / Rpim(I) all: 0.069 / Net I/σ(I): 12.8
Reflection shellResolution: 1.76→1.82 Å / Redundancy: 7.7 % / Num. unique obs: 4392 / Rpim(I) all: 0.663 / % possible all: 98

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Processing

Software
NameClassification
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5V1Y

5v1y


Resolution: 1.76→29.947 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 22.13
RfactorNum. reflection% reflection
Rfree0.2071 2016 4.35 %
Rwork0.1727 --
obs0.1743 46327 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.76→29.947 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3215 0 36 248 3499
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113405
X-RAY DIFFRACTIONf_angle_d1.1574579
X-RAY DIFFRACTIONf_dihedral_angle_d20.551332
X-RAY DIFFRACTIONf_chiral_restr0.071491
X-RAY DIFFRACTIONf_plane_restr0.009597
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7458-1.78940.26321380.27812985X-RAY DIFFRACTION93
1.7894-1.83780.28171460.24533096X-RAY DIFFRACTION98
1.8378-1.89190.25351460.22853163X-RAY DIFFRACTION98
1.8919-1.95290.26811300.22933181X-RAY DIFFRACTION100
1.9529-2.02270.24841430.19193200X-RAY DIFFRACTION99
2.0227-2.10370.27281370.18393162X-RAY DIFFRACTION99
2.1037-2.19940.21431560.17783201X-RAY DIFFRACTION100
2.1994-2.31530.20651360.16273185X-RAY DIFFRACTION100
2.3153-2.46030.20071440.16923172X-RAY DIFFRACTION100
2.4603-2.65020.23271440.17273202X-RAY DIFFRACTION100
2.6502-2.91670.21781500.17253195X-RAY DIFFRACTION100
2.9167-3.33830.21791520.17013184X-RAY DIFFRACTION100
3.3383-4.2040.16161440.14693215X-RAY DIFFRACTION100
4.204-29.95170.1831500.1643170X-RAY DIFFRACTION100

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