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- PDB-1j8c: Solution Structure of the Ubiquitin-like Domain of hPLIC-2 -

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Basic information

Entry
Database: PDB / ID: 1j8c
TitleSolution Structure of the Ubiquitin-like Domain of hPLIC-2
Componentsubiquitin-like protein hPLIC-2
KeywordsSTRUCTURAL GENOMICS / ubiquitin-like domain
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 proteasomal ubiquitin-dependent protein catabolic process / regulation of autophagosome assembly / autophagosome assembly / autophagosome / polyubiquitin modification-dependent protein binding / regulation of macroautophagy / ERAD pathway ...negative regulation of G protein-coupled receptor internalization / negative regulation of clathrin-dependent endocytosis / positive regulation of ERAD pathway / regulation of proteasomal ubiquitin-dependent protein catabolic process / regulation of autophagosome assembly / autophagosome assembly / autophagosome / polyubiquitin modification-dependent protein binding / regulation of macroautophagy / ERAD pathway / molecular condensate scaffold activity / Cargo recognition for clathrin-mediated endocytosis / cytoplasmic vesicle / ubiquitin-dependent protein catabolic process / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / 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 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) ...: / 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 / 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 / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsWalters, K.J. / Kleijnen, M.F. / Goh, A.M. / Wagner, G. / Howley, P.M.
CitationJournal: Biochemistry / Year: 2002
Title: Structural studies of the interaction between ubiquitin family proteins and proteasome subunit S5a.
Authors: Walters, K.J. / Kleijnen, M.F. / Goh, A.M. / Wagner, G. / Howley, P.M.
History
DepositionMay 21, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999SEQUENCE The C-terminus residues 104-125 were added as linker and his tag for ease of purification.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ubiquitin-like protein hPLIC-2


Theoretical massNumber of molelcules
Total (without water)13,6371
Polymers13,6371
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 / 20all calculated structures submitted
RepresentativeModel #12lowest energy

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Components

#1: Protein ubiquitin-like protein hPLIC-2


Mass: 13637.364 Da / Num. of mol.: 1 / Fragment: N-terminal domain (residues 1-103)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9UHD9

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1213D 15N-separated NOESY
1313D 13C-separated NOESY
NMR detailsText: This structure was determined by using standard triple-resonance NMR spectroscopy.

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Sample preparation

DetailsContents: 1.0 mM protein / Solvent system: 50 mM NaPO4 (pH 6.5) 100 mM NaCl
Sample conditionsIonic strength: 100 mM NaCl / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Varian INOVAVarianINOVA5002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851Brungerstructure solution
X-PLOR3.851Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on 983 NOE-derived distance restraints, 44 dihedral angle restraints, 23 hydrogen bonds
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20

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