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- PDB-5v1y: Crystal structure of the ternary RPN13 PRU-RPN2 (940-953)-ubiquit... -

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Basic information

Entry
Database: PDB / ID: 5v1y
TitleCrystal structure of the ternary RPN13 PRU-RPN2 (940-953)-ubiquitin complex
Components
  • 26S proteasome non-ATPase regulatory subunit 1
  • Proteasomal ubiquitin receptor ADRM1
  • Ubiquitin
KeywordsPROTEIN BINDING / RPN13 / proteasome / RPN2 / ubiquitin
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 / mitochondrion transport along microtubule / 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 / mitochondrion transport along microtubule / Cross-presentation of soluble exogenous antigens (endosomes) / fat pad development / Somitogenesis / female gonad development / proteasome binding / molecular function inhibitor activity / seminiferous tubule development / regulation of protein catabolic process / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / proteasome storage granule / endopeptidase activator activity / proteasome assembly / regulation of proteasomal protein catabolic process / enzyme regulator activity / energy homeostasis / regulation of neuron apoptotic 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 / 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 / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / 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 / InlA-mediated entry of Listeria monocytogenes into host cells / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / Translesion synthesis by REV1 / NF-kB is activated and signals survival / Regulation of PTEN localization / Translesion synthesis by POLK / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / proteasome complex / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / 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 / neuron projection morphogenesis / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / regulation of mitochondrial membrane potential / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / positive regulation of protein ubiquitination / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / Regulation of NF-kappa B signaling / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / Negative regulators of DDX58/IFIH1 signaling / TNFR2 non-canonical NF-kB pathway / NOTCH3 Activation and Transmission of Signal to the Nucleus / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4
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-B / Proteasomal ubiquitin receptor ADRM1 / 26S proteasome non-ATPase regulatory subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.421 Å
AuthorsHemmis, C.W. / VanderLinden, R.T. / Yao, T. / Robinson, H. / Hill, C.P.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM059135 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R21 CA191929 United States
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structure and energetics of pairwise interactions between proteasome subunits RPN2, RPN13, and ubiquitin clarify a substrate recruitment mechanism.
Authors: VanderLinden, R.T. / Hemmis, C.W. / Yao, T. / Robinson, H. / Hill, C.P.
History
DepositionMar 2, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1May 10, 2017Group: Database references
Revision 1.2Jun 21, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)47,8366
Polymers47,8366
Non-polymers00
Water9,170509
1
A: Proteasomal ubiquitin receptor ADRM1
C: Ubiquitin
E: 26S proteasome non-ATPase regulatory subunit 1


Theoretical massNumber of molelcules
Total (without water)23,9183
Polymers23,9183
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Proteasomal ubiquitin receptor ADRM1
D: Ubiquitin
F: 26S proteasome non-ATPase regulatory subunit 1


Theoretical massNumber of molelcules
Total (without water)23,9183
Polymers23,9183
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.129, 96.098, 57.605
Angle α, β, γ (deg.)90.00, 96.38, 90.00
Int Tables number4
Space group name H-MP1211

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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: 13482.367 Da / Num. of mol.: 2 / Fragment: PRU domain (UNP residues 19-132)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADRM1, GP110 / Plasmid: pET151 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 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: UBB / Plasmid: pET3a / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 RIL / References: UniProt: P0CG47
#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: 1858.906 Da / Num. of mol.: 2 / Fragment: C-termimal domain (UNP residues 940-953)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD1 / Plasmid: pET151 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 RIL / References: UniProt: Q99460
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 509 / 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: 2.08 Å3/Da / Density % sol: 40.79 %
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
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.42→50 Å / Num. obs: 72405 / % possible obs: 98 % / Redundancy: 7.6 % / Rsym value: 0.066 / Net I/σ(I): 24.8
Reflection shellResolution: 1.42→1.47 Å / Redundancy: 7 % / Mean I/σ(I) obs: 5.2 / Num. unique all: 2526 / Num. unique obs: 2526 / Rsym value: 0.349 / % possible all: 93

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 2R2Y & 1CMX

2r2y

1cmx


Resolution: 1.421→36.804 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 15.72
RfactorNum. reflection% reflection
Rfree0.1748 3662 5.06 %
Rwork0.1396 --
obs0.1413 72405 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.421→36.804 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3246 0 0 509 3755
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083387
X-RAY DIFFRACTIONf_angle_d0.9844581
X-RAY DIFFRACTIONf_dihedral_angle_d16.1591335
X-RAY DIFFRACTIONf_chiral_restr0.086493
X-RAY DIFFRACTIONf_plane_restr0.007603
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4206-1.43930.1891390.13792526X-RAY DIFFRACTION94
1.4393-1.4590.20461570.13112546X-RAY DIFFRACTION97
1.459-1.47980.17281190.12562620X-RAY DIFFRACTION97
1.4798-1.50190.17661320.13062628X-RAY DIFFRACTION97
1.5019-1.52540.18951320.1212591X-RAY DIFFRACTION98
1.5254-1.55040.16231350.11952614X-RAY DIFFRACTION98
1.5504-1.57710.16341360.1172659X-RAY DIFFRACTION98
1.5771-1.60580.21171510.12272572X-RAY DIFFRACTION98
1.6058-1.63670.1721340.12372611X-RAY DIFFRACTION98
1.6367-1.67010.1851650.12392611X-RAY DIFFRACTION98
1.6701-1.70640.17031410.11952659X-RAY DIFFRACTION98
1.7064-1.74610.15691440.12362646X-RAY DIFFRACTION99
1.7461-1.78980.17531610.12262584X-RAY DIFFRACTION99
1.7898-1.83820.16511470.12322636X-RAY DIFFRACTION99
1.8382-1.89230.17321490.12742677X-RAY DIFFRACTION99
1.8923-1.95330.18591400.12752641X-RAY DIFFRACTION99
1.9533-2.02310.15931270.13062684X-RAY DIFFRACTION99
2.0231-2.10410.14351340.12492676X-RAY DIFFRACTION99
2.1041-2.19990.17071450.13112651X-RAY DIFFRACTION100
2.1999-2.31590.15081260.12972715X-RAY DIFFRACTION100
2.3159-2.46090.16931550.13962656X-RAY DIFFRACTION100
2.4609-2.65090.1751500.14812680X-RAY DIFFRACTION100
2.6509-2.91760.19211550.15222677X-RAY DIFFRACTION100
2.9176-3.33950.19971180.15492735X-RAY DIFFRACTION100
3.3395-4.20640.16661410.14182684X-RAY DIFFRACTION100
4.2064-36.81630.18311290.15892764X-RAY DIFFRACTION100

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