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- PDB-2kqz: Solution structure of the Rpn13 DEUBAD domain -

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Basic information

Entry
Database: PDB / ID: 2kqz
TitleSolution structure of the Rpn13 DEUBAD domain
ComponentsProteasomal ubiquitin receptor ADRM1
KeywordsPROTEIN BINDING / PROTEASOME / UCH37-BINDING DOMAIN
Function / homology
Function and homology information


proteasome regulatory particle, lid subcomplex / molecular function inhibitor activity / proteasome binding / endopeptidase activator activity / proteasome assembly / proteasome complex / transcription elongation by RNA polymerase II / UCH proteinases / protease binding / proteasome-mediated ubiquitin-dependent protein catabolic process ...proteasome regulatory particle, lid subcomplex / molecular function inhibitor activity / proteasome binding / endopeptidase activator activity / proteasome assembly / proteasome complex / transcription elongation by RNA polymerase II / UCH proteinases / protease binding / proteasome-mediated ubiquitin-dependent protein catabolic process / Ub-specific processing proteases / nucleoplasm / plasma membrane / cytosol
Similarity search - Function
uronate isomerase, domain 2, chain A - #20 / uronate isomerase, domain 2, chain A / 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 ...uronate isomerase, domain 2, chain A - #20 / uronate isomerase, domain 2, chain A / 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. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Proteasomal ubiquitin receptor ADRM1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsChen, X. / Lee, B. / Finley, D. / Walters, K.J.
CitationJournal: Mol.Cell / Year: 2010
Title: Structure of Proteasome Ubiquitin Receptor hRpn13 and Its Activation by the Scaffolding Protein hRpn2.
Authors: Chen, X. / Lee, B.H. / Finley, D. / Walters, K.J.
History
DepositionNov 25, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 23, 2015Group: Structure summary
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Proteasomal ubiquitin receptor ADRM1


Theoretical massNumber of molelcules
Total (without water)16,2761
Polymers16,2761
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)35 / 35all calculated structures submitted
RepresentativeModel #1lowest energy

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Components

#1: Protein Proteasomal ubiquitin receptor ADRM1 / Adhesion-regulating molecule 1 / ARM-1 / 110 kDa cell membrane glycoprotein / Gp110 / Rpn13 homolog ...Adhesion-regulating molecule 1 / ARM-1 / 110 kDa cell membrane glycoprotein / Gp110 / Rpn13 homolog / Proteasome regulatory particle non-ATPase 13 / hRpn13


Mass: 16276.110 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 BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q16186

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCA
1313D HN(CO)CA
1413D HNCO
1513D HN(CO)CA
1613D (H)CCH-TOCSY
1712D 1H-15N HSQC
1813D HN(CA)CB
1912D 1H-1H NOESY
11032D 1H-1H NOESY
11122D 1H-13C HSQC
11223D 1H-13C NOESY
11312D 1H-15N HSQC
11413D 1H-15N NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.7 mM [U-100% 13C; U-100% 15N; U-70% 2H] XCCD, 0.7 mM [U-15N; U-50% 2H] XCCD, 0.7 mM [U-15N; 100% 2H] XCCD, 0.5 mM [U-15N] XCCD, 1.0 mM XCCD, 90% H2O/10% D2O90% H2O/10% D2O
20.7 mM [U-13C] XCCD, 100% D2O100% D2O
31.0 mM XCCD, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMXCCD-1[U-100% 13C; U-100% 15N; U-70% 2H]1
0.7 mMXCCD-2[U-15N; U-50% 2H]1
0.7 mMXCCD-3[U-15N; 100% 2H]1
0.5 mMXCCD-4[U-15N]1
1.0 mMXCCD-51
0.7 mMXCCD-6[U-13C]2
1.0 mMXCCD-73
Sample conditionsIonic strength: 20 mM phosphate, 50 mM NaCl / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002
Varian INOVAVarianINOVA9003

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Processing

NMR software
NameVersionDeveloperClassification
VnmrJVariancollection
NMRPipe2.5Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XEASY6.4Bartels et al.chemical shift assignment
XEASY6.4Bartels et al.data analysis
XEASY6.4Bartels et al.peak picking
CARA1.8.4Keller and Wuthrichchemical shift assignment
CARA1.8.4Keller and Wuthrichdata analysis
CARA1.8.4Keller and Wuthrichpeak picking
X-PLOR NIH2.24Schwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIH2.24Schwieters, Kuszewski, Tjandra and Clorestructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 2721 restraints, 2503 are NOE-derived distance constraints, 76 distance restraints from hydrogen bonds, 142 dihedral angle restraints.
NMR constraintsNOE constraints total: 2503 / NOE intraresidue total count: 963 / NOE long range total count: 340 / NOE medium range total count: 645 / NOE sequential total count: 555 / Hydrogen bond constraints total count: 76 / Protein phi angle constraints total count: 71 / Protein psi angle constraints total count: 71
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 35 / Conformers submitted total number: 35

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