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- PDB-1p1a: NMR structure of ubiquitin-like domain of hHR23B -

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Basic information

Entry
Database: PDB / ID: 1p1a
TitleNMR structure of ubiquitin-like domain of hHR23B
ComponentsUV excision repair protein RAD23 homolog B
KeywordsDNA BINDING PROTEIN / UBIQUITIN-LIKE
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 / proteasome complex / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle ...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 / proteasome complex / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / ubiquitin binding / nucleotide-excision repair / DNA Damage Recognition in GG-NER / Formation of Incision Complex in GG-NER / single-stranded DNA binding / spermatogenesis / proteasome-mediated ubiquitin-dependent protein catabolic process / RNA polymerase II-specific DNA-binding transcription factor binding / damaged DNA 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 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
UV excision repair protein RAD23 homolog B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / Cyana-Automated NOE assignment, Torsion angle dynamics; Amber-Simulated annealing, Cyana output is the initial structure
AuthorsRyu, K.S. / Lee, K.J. / Bae, S.H. / Kim, B.K. / Kim, K.A. / Choi, B.S.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Binding surface mapping of intra- and interdomain interactions among hHR23B, ubiquitin, and polyubiquitin binding site 2 of S5a
Authors: Ryu, K.S. / Lee, K.J. / Bae, S.H. / Kim, B.K. / Kim, K.A. / Choi, B.S.
History
DepositionApr 11, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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 / 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
Revision 1.4May 29, 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: UV excision repair protein RAD23 homolog B


Theoretical massNumber of molelcules
Total (without water)9,5241
Polymers9,5241
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)14 / 60structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein UV excision repair protein RAD23 homolog B / RAD23 / hHR23B


Mass: 9524.032 Da / Num. of mol.: 1 / Fragment: Ubiquitin-like domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: hHR23B / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P54727

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111CBCA(CO)NH, HN(CA)CB, CCC-TOC-NNH, HCC-TOC-NNH, HNCO
1223D 15N-separated TOCSY, Intensity-MODULATED 15N HSQC
1332D NOESY
NMR detailsText: Distance Restraints From 2D D2O-NOESY, 3D 15N-NOESY-HSQC, Angle Restaints From Intensity-modulated 15N HSQC and Talos Chemical shift analysis

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM UbL domain 15N,13C; 50mM Sodium Phosphate Buffer with 100mM NaCl92.5% H2O, 7.5% D2O
22mM UbL domain 15N; 50mM Sodium Phosphate Buffer with 100mM NaCl92.5% H2O, 7.5% D2O
32mM UbL domain non-labeled; 50mM Sodium Phosphate Buffer with 100mM NaCl100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150mM sodium phosphate + 100mM sodium chloride 6ambient 303 K
250mM sodium phosphate + 100mM sodium chloride 6ambient 303 K
350mM sodium phosphate + 100mM sodium chloride 6ambient 303 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionClassification
CYANA1.0.6structure solution
Amber7refinement
RefinementMethod: Cyana-Automated NOE assignment, Torsion angle dynamics; Amber-Simulated annealing, Cyana output is the initial structure
Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 60 / Conformers submitted total number: 14

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