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- PDB-1f4i: SOLUTION STRUCTURE OF THE HHR23A UBA(2) MUTANT P333E, DEFICIENT I... -

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Basic information

Entry
Database: PDB / ID: 1f4i
TitleSOLUTION STRUCTURE OF THE HHR23A UBA(2) MUTANT P333E, DEFICIENT IN BINDING THE HIV-1 ACCESSORY PROTEIN VPR
ComponentsUV EXCISION REPAIR PROTEIN PROTEIN RAD23 HOMOLOG A
KeywordsDNA BINDING PROTEIN / TRANSCRIPTION / alpha 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 / DNA Damage Recognition in GG-NER / protein destabilization / 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 / cytoplasm / 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. / 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
MethodSOLUTION NMR / simulated annealing, distance geometry
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.Y. / Feigon, J.
History
DepositionJun 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: 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 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: UV EXCISION REPAIR PROTEIN PROTEIN RAD23 HOMOLOG A


Theoretical massNumber of molelcules
Total (without water)5,1841
Polymers5,1841
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)21 / 100structures with the lowest energy
RepresentativeModel #12lowest energy

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Components

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


Mass: 5183.710 Da / Num. of mol.: 1 / Fragment: C-TERMINAL UBA DOMAIN / Mutation: P333E / Source method: obtained synthetically
Details: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THIS PEPTIDE NATURALLY OCCURS IN HUMANS (HOMO SAPIENS).
References: UniProt: P54725

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques

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Sample preparation

DetailsContents: 2mM UBA(2) domain mutant P333E; 50mM phosphate buffer, 150mM sodium chloride; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 50mM sodium phosphate, 150mM sodium chloride
pH: 6.5 / Pressure: ambient / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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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
XwinNMR2.6Bruker, Karlsruheprocessing
XEASY1.3.10Bartelsdata analysis
X-PLOR3.1Brungerrefinement
X-PLOR3.1Brungerstructure solution
RefinementMethod: simulated annealing, distance geometry / Software ordinal: 1
Details: total number of restraints 826, 204 intraresidual, 182 sequential, 226 medium range (|i-j|<5), 214 long range (|i-j|>=5)
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 21

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