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- PDB-1dv0: Refined NMR solution structure of the C-terminal UBA domain of th... -

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Basic information

Entry
Database: PDB / ID: 1dv0
TitleRefined NMR solution structure of the C-terminal UBA domain of the human homologue of RAD23A (HHR23A)
ComponentsDNA REPAIR PROTEIN HHR23A
KeywordsDNA BINDING PROTEIN / Helical bundle
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 / protein destabilization / DNA Damage Recognition in GG-NER / kinase binding / Formation of Incision Complex in GG-NER / 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 domain profile. / Ubiquitin-like domain / 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, molecular dynamics
AuthorsWithers-Ward, E.S. / Mueller, T.D. / Chen, I.S. / Feigon, J.
Citation
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.
#1: Journal: Nat.Struct.Biol. / Year: 1998
Title: Structure of a Human DNA Repair Protein UBA Domain that Interacts with HIV-1 Vpr
Authors: Dieckmann, T. / Withers-Ward, E.S. / Jarosinski, M.A. / Liu, C.F. / Chen, I.S. / Feigon, J.
History
DepositionJan 19, 2000Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 11, 2000ID: 1UBA
Revision 1.0Feb 11, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 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
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA REPAIR PROTEIN HHR23A


Theoretical massNumber of molelcules
Total (without water)5,2961
Polymers5,2961
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)18 / 100structures with favorable non-bond energy, structures with the least restraint violations, structures with the lowest energy
RepresentativeModel #6closest to the average

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Components

#1: Protein/peptide DNA REPAIR PROTEIN HHR23A


Mass: 5295.841 Da / Num. of mol.: 1 / Fragment: UBA DOMAIN (C-TERMINAL DOMAIN)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGEX-2T (PHARMACIA) / Production host: Escherichia coli (E. coli) / 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
141DQF-COSY
NMR detailsText: This structure was determined using triple-resonance NMR spectroscopy

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM Uba-domain, chemically synthesized; 50mM potassium phosphate pH 6.5; 90% H2O, 10% D2O90% H2O/10% D2O
22mM Uba-domain, expressed in E.coli, 50mM sodium phosphate, 100mM sodium chloride, 95% H2O, 5% D2O95% H2O/5% D2O
32mM Uba-domain, U-15N, 50mM sodium phosphate, 100mM sodium chloride, 95% H2O, 5% D2O95% H2O/5% D2O
42mM Uba-domain, U-15N,13C, 50mM sodium phosphate, 100mM sodium chloride, 95% H2O, 5% D2O95% H2O/5% D2O
Sample conditionsIonic strength: 50mM sodium phosphate, 100mM sodium chloride
pH: 6.5 / Pressure: ambient / Temperature: 300 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX5002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR1.3Brukerprocessing
XEASY1.3.10Bartels, Xia, Billeter, Guntert, Wuthrichdata analysis
X-PLOR3.1Brungerstructure solution
X-PLOR3.1Brungerrefinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
Details: The structures are based on a total of 796 restraints, 779 are NOE-derived, 17 distance restraints are from hydrogen bonds
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with favorable non-bond energy, structures with the least restraint violations, structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 18

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