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- PDB-1ify: Solution Structure of the Internal UBA Domain of HHR23A -

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Basic information

Entry
Database: PDB / ID: 1ify
TitleSolution Structure of the Internal UBA Domain of HHR23A
ComponentsUV EXCISION REPAIR PROTEIN RAD23 HOMOLOG A
KeywordsDNA BINDING PROTEIN / Ubiquitin associated domain / UBA domain / Ubiquitin proteosome pathway
Function / homology
Function and homology information


regulation of proteasomal ubiquitin-dependent protein catabolic process / proteasome binding / ubiquitin-specific protease binding / polyubiquitin modification-dependent protein binding / positive regulation of viral genome replication / positive regulation of cell cycle / proteasome complex / Josephin domain DUBs / ubiquitin binding / nucleotide-excision repair ...regulation of proteasomal ubiquitin-dependent protein catabolic process / proteasome binding / ubiquitin-specific protease binding / polyubiquitin modification-dependent protein binding / positive regulation of viral genome replication / positive regulation of cell cycle / proteasome complex / Josephin domain DUBs / ubiquitin binding / nucleotide-excision repair / DNA Damage Recognition in GG-NER / protein destabilization / Formation of Incision Complex in GG-NER / kinase binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / single-stranded DNA binding / proteasome-mediated ubiquitin-dependent protein catabolic process / damaged DNA binding / intracellular membrane-bounded organelle / Golgi apparatus / protein-containing complex / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
RAD23A/RAD23B, UBA1 domain / UV excision repair protein Rad23 / XPC-binding domain / XPC-binding domain superfamily / XPC-binding domain / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / Ubiquitin-associated (UBA) domain / UBA/TS-N domain / Ubiquitin associated domain ...RAD23A/RAD23B, UBA1 domain / UV excision repair protein Rad23 / XPC-binding domain / XPC-binding domain superfamily / XPC-binding domain / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / Ubiquitin-associated (UBA) domain / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Helicase, Ruva Protein; domain 3 / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
UV excision repair protein RAD23 homolog A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsMueller, T.D. / Feigon, J.
Citation
Journal: J.Mol.Biol. / Year: 2002
Title: Solution structures of UBA domains reveal a conserved hydrophobic surface for protein-protein interactions.
Authors: Mueller, T.D. / Feigon, J.
#1: Journal: Biochemistry / Year: 2000
Title: Biochemical and Structural Analysis of the Interaction between the Uba(2) Domain of the DNA Repair Protein Hhr23A and HIV-1 Vpr
Authors: Withers-Ward, E.S. / Mueller, T.D. / Chen, I.S. / Feigon, J.
History
DepositionApr 13, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 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: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UV EXCISION REPAIR PROTEIN RAD23 HOMOLOG A


Theoretical massNumber of molelcules
Total (without water)5,4961
Polymers5,4961
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)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide UV EXCISION REPAIR PROTEIN RAD23 HOMOLOG A / HHR23A


Mass: 5496.235 Da / Num. of mol.: 1 / Fragment: INTERNAL UBA DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Star / References: UniProt: P54725

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Experimental details

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Experiment

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

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM UBA1 U-15N,13C50mM phosphate buffer, 100mM sodium chloride 95% H2O, 5% D2O
22mM UBA1 U-15N50mM phosphate buffer, 100mM sodium chloride 95% H2O, 5% D2O
32mM UBA150mM phosphate buffer, 100mM sodium chloride 95% H2O, 5% D2O
Sample conditionsIonic strength: 50mM sodium phosphate, 100mM sodium chloride
pH: 6.5 / Pressure: ambient / Temperature: 300 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 spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Bruker AGcollection
XwinNMR2.6Bruker AGprocessing
AURELIA2.8.9Bruker AGdata analysis
X-PLOR3.1Brungerstructure solution
X-PLOR3.1Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on 1692 NOE-derived distance restraints, of which 1055 distance restraints are non-redundant. 407 restraints are intraresidue, 212 are sequential, 226 are ...Details: The structures are based on 1692 NOE-derived distance restraints, of which 1055 distance restraints are non-redundant. 407 restraints are intraresidue, 212 are sequential, 226 are mediumrange (i-j < 5) and 210 are long-range (i-j > 4)
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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