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- PDB-2nbv: Solution structure of the Rpn13 Pru domain engaging the hPLIC2 UB... -

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Basic information

Entry
Database: PDB / ID: 2nbv
TitleSolution structure of the Rpn13 Pru domain engaging the hPLIC2 UBL domain
Components
  • Proteasomal ubiquitin receptor ADRM1
  • Ubiquilin-2
KeywordsPROTEIN BINDING
Function / homology
Function and homology information


negative regulation of G protein-coupled receptor internalization / negative regulation of clathrin-dependent endocytosis / positive regulation of ERAD pathway / regulation of autophagosome assembly / proteasome regulatory particle, lid subcomplex / molecular function inhibitor activity / proteasome binding / endopeptidase activator activity / autophagosome assembly / autophagosome ...negative regulation of G protein-coupled receptor internalization / negative regulation of clathrin-dependent endocytosis / positive regulation of ERAD pathway / regulation of autophagosome assembly / proteasome regulatory particle, lid subcomplex / molecular function inhibitor activity / proteasome binding / endopeptidase activator activity / autophagosome assembly / autophagosome / polyubiquitin modification-dependent protein binding / proteasome assembly / regulation of macroautophagy / ERAD pathway / proteasome complex / molecular condensate scaffold activity / transcription elongation by RNA polymerase II / UCH proteinases / Cargo recognition for clathrin-mediated endocytosis / cytoplasmic vesicle / ubiquitin-dependent protein catabolic process / protease binding / proteasome-mediated ubiquitin-dependent protein catabolic process / Ub-specific processing proteases / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
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 ...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. / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / PH-domain like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / 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
Proteasomal ubiquitin receptor ADRM1 / Ubiquilin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsChen, X. / Walters, K.J.
CitationJournal: Structure / Year: 2016
Title: Structures of Rpn1 T1:Rad23 and hRpn13:hPLIC2 Reveal Distinct Binding Mechanisms between Substrate Receptors and Shuttle Factors of the Proteasome.
Authors: Chen, X. / Randles, L. / Shi, K. / Tarasov, S.G. / Aihara, H. / Walters, K.J.
History
DepositionMar 12, 2016Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2016Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Proteasomal ubiquitin receptor ADRM1
B: Ubiquilin-2


Theoretical massNumber of molelcules
Total (without water)25,5062
Polymers25,5062
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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: 16742.045 Da / Num. of mol.: 1 / Fragment: residues 1-150
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: Protein Ubiquilin-2 / Chap1 / DSK2 homolog / Protein linking IAP with cytoskeleton 2 / PLIC-2 / hPLIC-2 / Ubiquitin-like ...Chap1 / DSK2 homolog / Protein linking IAP with cytoskeleton 2 / PLIC-2 / hPLIC-2 / Ubiquitin-like product Chap1/Dsk2


Mass: 8764.189 Da / Num. of mol.: 1 / Fragment: residues 26-103
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBQLN2, N4BP4, PLIC2, HRIHFB2157 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UHD9

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-15N HSQC
1332D 1H-15N HSQC
1433D 1H-15N NOESY
1543D 1H-15N NOESY
1652D 1H-13C HSQC
1753D 1H-13C NOESY aliphatic

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Sample preparation

Details
Solution-IDContentsSolvent system
10.3 mM [U-100% 15N] protein_1, 0.04-0.6 mM protein_2, 20 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 0.1 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
20.04-0.6 mM protein_1, 0.3 mM [U-100% 15N] protein_2, 20 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 0.1 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
30.5 mM protein_1, 0.5 mM [U-100% 15N, 100% Deuterium] protein_2, 20 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 0.1 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
40.5 mM [U-100% 15N, 100% Deuterium] protein_2, 20 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 0.1 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
50.5 mM [U-13C] protein_1, 0.5 mM [U-100% 15N, 100% Deuterium] protein_2,20 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 0.1 % sodium azide, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
0.3 mMentity_1-1[U-100% 15N]1
mMentity_2-20.04-0.61
20 mMsodium phosphate-31
50 mMsodium chloride-41
2 mMDTT-51
0.1 %sodium azide-61
mMentity_1-70.04-0.62
0.3 mMentity_2-8[U-100% 15N]2
20 mMsodium phosphate-92
50 mMsodium chloride-102
2 mMDTT-112
0.1 %sodium azide-122
0.5 mMentity_1-133
0.5 mMentity_2-14[U-100% 15N, 100% Deuterium]3
20 mMsodium phosphate-153
50 mMsodium chloride-163
2 mMDTT-173
0.1 %sodium azide-183
0.5 mMentity_2-19[U-100% 15N, 100% Deuterium]4
20 mMsodium phosphate-204
50 mMsodium chloride-214
2 mMDTT-224
0.1 %sodium azide-234
0.5 mMentity_1-24[U-13C]5
0.5 mMentity_2-25[U-100% 15N, 100% Deuterium]5
20 mMsodium phosphate-265
50 mMsodium chloride-275
2 mMDTT-285
0.1 %sodium azide-295
Sample conditionsIonic strength: 50 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Bruker AvanceBrukerAVANCE8502

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Processing

NMR software
NameVersionDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XEASYBartels et al.peak picking
XEASYBartels et al.data analysis
XEASYBartels et al.chemical shift assignment
HADDOCK2.2Alexandre Bonvinrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
ProcheckNMRLaskowski and MacArthurdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The starting structures are PDB enries 1J8C and 5IRS.
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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