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- PDB-2mkz: solution structure of a protein C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 2mkz
Titlesolution structure of a protein C-terminal 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 / proteasome-mediated ubiquitin-dependent protein catabolic process / protease binding ...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 / proteasome-mediated ubiquitin-dependent protein catabolic process / protease binding / 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 / molecular dynamics, simulated annealing
Model detailslowest energy, model1
AuthorsFeng, Y. / Jiao, L.
CitationJournal: Protein Cell / Year: 2014
Title: Mechanism of the Rpn13-induced activation of Uch37
Authors: Jiao, L. / Ouyang, S. / Shaw, N. / Song, G. / Feng, Y. / Niu, F. / Qiu, W. / Zhu, H. / Hung, L.W. / Zuo, X. / Eleonora Shtykova, V. / Zhu, P. / Dong, Y.H. / Xu, R. / Liu, Z.J.
History
DepositionFeb 17, 2014Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Dec 31, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details
Revision 1.2May 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


Theoretical massNumber of molelcules
Total (without water)14,8231
Polymers14,8231
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures 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: 14822.517 Da / Num. of mol.: 1 / Fragment: UNP residues 270-407
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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCA
1413D HN(CA)CB
1513D CBCA(CO)NH
1613D HNCO
1713D HN(CA)CO
1813D HBHA(CO)NH
1913D HBHANH
11013D (H)CCH-TOCSY
11113D CCH-TOCSY
11213D 1H-15N NOESY
11313D 1H-13C NOESY aliphatic
11413D 1H-13C NOESY aromatic

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Sample preparation

DetailsContents: 0.5-1.0 mM [U-13C; U-15N] entity-1, 40 mM sodium phosphate-2, 20 mM potassium chloride-3, 0.02 % DSS-4, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMentity-1[U-13C; U-15N]0.5-1.01
40 mMsodium phosphate-21
20 mMpotassium chloride-31
0.02 %DSS-41
Sample conditionsIonic strength: 80 / pH: 6.5 / Pressure: ambient atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
XwinNMRBruker Biospincollection
FelixAccelrys Software Inc.processing
FelixAccelrys Software Inc.chemical shift assignment
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
SANEDuggan, Legge, Dyson & Wrightrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: molecular dynamics, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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