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- PDB-9vff: Solution structure of XPC binding domain of a hHR23B variant - H2... -

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Basic information

Entry
Database: PDB / ID: 9vff
TitleSolution structure of XPC binding domain of a hHR23B variant - H274N/H323Q
ComponentsUV excision repair protein RAD23 homolog B
KeywordsMETAL BINDING PROTEIN / metal-binding dead mutant
Function / homology
Function and homology information


XPC complex / DNA damage sensor activity / regulation of proteasomal ubiquitin-dependent protein catabolic process / cellular response to interleukin-7 / proteasome binding / polyubiquitin modification-dependent protein binding / embryonic organ development / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / proteasome complex ...XPC complex / DNA damage sensor activity / regulation of proteasomal ubiquitin-dependent protein catabolic process / cellular response to interleukin-7 / proteasome binding / polyubiquitin modification-dependent protein binding / embryonic organ development / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / proteasome complex / ubiquitin binding / DNA Damage Recognition in GG-NER / nucleotide-excision repair / Formation of Incision Complex in GG-NER / single-stranded DNA binding / spermatogenesis / damaged DNA binding / proteasome-mediated ubiquitin-dependent protein catabolic process / RNA polymerase II-specific DNA-binding transcription factor binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / nucleoplasm / nucleus / cytosol
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. / UBA/TS-N domain / Ubiquitin associated 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. / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
UV excision repair protein RAD23 homolog B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / matrix relaxation
AuthorsXiao, T. / He, D. / Kelly, M.J.S. / Chang, C.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Mol.Cell / Year: 2025
Title: RAD23B acquires a copper metalloadaptor function in amphibian-to-reptile evolution to increase metabolism and regulate genomic integrity.
Authors: Xiao, T. / He, D. / Liu, D. / Jia, S. / Chen, Q. / Silverman, D. / Maitra, N. / Huang, A.Y. / Pezacki, A. / Nguyen, T.T. / Rao, G. / Tillage, R. / Deng, K. / Weinshenker, D. / Britt, R.D. / ...Authors: Xiao, T. / He, D. / Liu, D. / Jia, S. / Chen, Q. / Silverman, D. / Maitra, N. / Huang, A.Y. / Pezacki, A. / Nguyen, T.T. / Rao, G. / Tillage, R. / Deng, K. / Weinshenker, D. / Britt, R.D. / Kelly, M.J.S. / Dan, Y. / Chang, C.J.
History
DepositionJun 11, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UV excision repair protein RAD23 homolog B


Theoretical massNumber of molelcules
Total (without water)8,0371
Polymers8,0371
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 20structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein UV excision repair protein RAD23 homolog B / HR23B / hHR23B / XP-C repair-complementing complex 58 kDa protein / p58


Mass: 8036.942 Da / Num. of mol.: 1 / Mutation: H274N, H323Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAD23B / Production host: Escherichia coli (E. coli) / References: UniProt: P54727
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HNCA
121isotropic1CBCANH
131isotropic13D CBCA(CO)NH
141isotropic13D HBHA(CO)NH
151isotropic13D C(CO)NH
161isotropic23D (H)CCH-TOCSY
171isotropic23D 1H-13C NOESY
181isotropic23D 1H-15N NOESY
191isotropic22D 1H-15N HSQC

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Sample preparation

DetailsType: solution
Contents: 1.1 mM [U-100% 13C; U-100% 15N] UV excision repair protein RAD23 homolog B, 20 mM sodium phosphate, 160 mM sodium chloride, 5 % v/v [U-100% 2H] D2O, 95 % v/v H2O
Label: 13C, 15N_NQ / Solvent system: 5 % v/v [U-100% 2H] D2O, 95 % v/v H2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.1 mMUV excision repair protein RAD23 homolog B[U-100% 13C; U-100% 15N]1
20 mMsodium phosphatenatural abundance1
160 mMsodium chloridenatural abundance1
Sample conditionsIonic strength: 160 mM / Label: conditions_1 / pH: 7.4 / Pressure: 1 atm / Temperature: 300 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE NEOBrukerAVANCE NEO6001
Bruker AVANCE NEOBrukerAVANCE NEO8002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.98.15Guntert, Mumenthaler and Wuthrichchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
X-PLOR NIH3.7.0.1Schwieters, Kuszewski, Tjandra and Clorerefinement
ARTINA3.2Klukowski, P., Riek, R. and Guntert, P.peak picking
TopSpin4Bruker Biospincollection
TopSpin4.2Bruker Biospinprocessing
RefinementMethod: matrix relaxation / Software ordinal: 3
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 10

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