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- PDB-1tp4: Solution structure of the XPC binding domain of hHR23A protein -

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Basic information

Entry
Database: PDB / ID: 1tp4
TitleSolution structure of the XPC binding domain of hHR23A protein
ComponentsUV excision repair protein RAD23 homolog A
KeywordsDNA REPAIR / NER / XPC / Rad23
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
XPC-binding 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. / UBA/TS-N domain / Ubiquitin associated domain ...XPC-binding 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. / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Arc Repressor Mutant, subunit A / 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 / distance geometry
AuthorsKamionka, M. / Feigon, J.
CitationJournal: Protein Sci. / Year: 2004
Title: Structure of the XPC binding domain of hHR23A reveals hydrophobic patches for protein interaction
Authors: Kamionka, M. / Feigon, J.
History
DepositionJun 15, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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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)10,7831
Polymers10,7831
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)25 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein UV excision repair protein RAD23 homolog A / HHR23A


Mass: 10782.896 Da / Num. of mol.: 1 / Fragment: XPC binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAD23A / Plasmid: pGEX2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P54725

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
131E-COSY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

DetailsContents: 1mM XPCB U-15N,13C, 20mM sodium phosphate, 122mM sodium chloride, 0.05% sodium azide
Solvent system: 95% H2O/5% D2O
Sample conditionsIonic strength: 20mM sodium phosphate, 122mM sodium chloride, 0.05% sodium azide
pH: 7.3 / Pressure: ambient / Temperature: 298 K

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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: 600 MHz

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Processing

NMR software
NameVersionClassification
XwinNMR2.6collection
Felix2000data analysis
X-PLOR3.1structure solution
X-PLOR3.1refinement
RefinementMethod: distance geometry / Software ordinal: 1
Details: The structures are based on a total of 917 non-redundant NOE-derived distance constraints, 82 dihedral angle restraints and 42 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 25

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