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- PDB-2qsf: Crystal structure of the Rad4-Rad23 complex -

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Basic information

Entry
Database: PDB / ID: 2qsf
TitleCrystal structure of the Rad4-Rad23 complex
Components
  • DNA repair protein RAD4
  • UV excision repair protein RAD23
KeywordsDNA BINDING PROTEIN / ALPHA-BETA STRUCTURE / BETA HAIRPIN / TRANSGLUTAMINASE FOLD / DNA-DAMAGE RECOGNITION / DNA REPAIR / NUCLEOTIDE EXCISION REPAIR / XERODERMA PIGMENTOSUM
Function / homology
Function and homology information


PNGase complex / nucleotide-excision repair factor 2 complex / single-strand break-containing DNA binding / XPC complex / nucleotide-excision repair, DNA damage recognition / K48-linked polyubiquitin modification-dependent protein binding / proteasome binding / DNA topological change / polyubiquitin modification-dependent protein binding / mismatch repair ...PNGase complex / nucleotide-excision repair factor 2 complex / single-strand break-containing DNA binding / XPC complex / nucleotide-excision repair, DNA damage recognition / K48-linked polyubiquitin modification-dependent protein binding / proteasome binding / DNA topological change / polyubiquitin modification-dependent protein binding / mismatch repair / ERAD pathway / ubiquitin binding / nucleotide-excision repair / single-stranded DNA binding / protein-macromolecule adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / damaged DNA binding / negative regulation of transcription by RNA polymerase II / mitochondrion / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Rad4, beta-hairpin domain BHD3 / Rad4, beta-hairpin domain BHD1 / Rad4, beta-hairpin domain BHD2 / XPC-binding domain / DNA repair protein Rad4 / DNA repair protein Rad4, subgroup / Rad4/PNGase transglutaminase-like fold / Rad4 beta-hairpin domain 1 / Rad4 beta-hairpin domain 2 / Rad4 beta-hairpin domain 3 ...Rad4, beta-hairpin domain BHD3 / Rad4, beta-hairpin domain BHD1 / Rad4, beta-hairpin domain BHD2 / XPC-binding domain / DNA repair protein Rad4 / DNA repair protein Rad4, subgroup / Rad4/PNGase transglutaminase-like fold / Rad4 beta-hairpin domain 1 / Rad4 beta-hairpin domain 2 / Rad4 beta-hairpin domain 3 / Rad4, beta-hairpin domain 3 superfamily / Rad4 beta-hairpin domain 1 / Rad4 beta-hairpin domain 3 / Rad4 beta-hairpin domain 1 / Rad4 beta-hairpin domain 2 / Rad4 beta-hairpin domain 3 / Rad4 transglutaminase-like domain / Coagulation Factor XIII; Chain A, domain 2 / Transglutaminase-like / UV excision repair protein Rad23 / XPC-binding domain / XPC-binding domain superfamily / XPC-binding domain / Anthopleurin-A / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / Transglutaminase-like superfamily / Ubiquitin-associated (UBA) domain / UBA/TS-N domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Single Sheet / Helicase, Ruva Protein; domain 3 / Papain-like cysteine peptidase superfamily / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Arc Repressor Mutant, subunit A / Ubiquitin-like domain superfamily / Alpha-Beta Plaits / Alpha-Beta Complex / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA repair protein RAD4 / UV excision repair protein RAD23
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.35 Å
AuthorsMin, J.-H. / Pavletich, N.P.
CitationJournal: Nature / Year: 2007
Title: Recognition of DNA damage by the Rad4 nucleotide excision repair protein
Authors: Min, J.-H. / Pavletich, N.P.
History
DepositionJul 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 999 SEQUENCE DNA PLASMID SEQUENCING DATA CONFIRM THE REPORTED SEQUENCE OF CHAIN A

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA repair protein RAD4
X: UV excision repair protein RAD23


Theoretical massNumber of molelcules
Total (without water)79,9232
Polymers79,9232
Non-polymers00
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.167, 115.711, 113.947
Angle α, β, γ (deg.)90.00, 105.70, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein DNA repair protein RAD4 / Rad4


Mass: 62140.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RAD4 / Cell line (production host): Hi5 / Organ (production host): eggs / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P14736
#2: Protein UV excision repair protein RAD23 / Rad23


Mass: 17783.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RAD23 / Cell line (production host): Hi5 / Organ (production host): eggs / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P32628
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.31 Å3/Da / Density % sol: 62.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM sodium phosphate, 8% (w/v) PEG 2000, 2 mM dithiothreitol, pH 6.5, hanging-drop vapor diffusion, temperature 277K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97922 / Wavelength: 0.97922 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 24, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97922 Å / Relative weight: 1
ReflectionResolution: 2.35→15 Å / Num. obs: 41336

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3data extraction
RefinementResolution: 2.35→15 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1566 3.6 %random
Rwork0.226 ---
obs-38988 90.5 %-
Solvent computationBsol: 43.555 Å2
Displacement parametersBiso mean: 56.749 Å2
Baniso -1Baniso -2Baniso -3
1-11.357 Å20 Å27.839 Å2
2---20.288 Å20 Å2
3---8.931 Å2
Refinement stepCycle: LAST / Resolution: 2.35→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4826 0 0 248 5074
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.192
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water.param

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