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- PDB-2qsg: Crystal structure of Rad4-Rad23 bound to a UV-damaged DNA -

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Basic information

Entry
Database: PDB / ID: 2qsg
TitleCrystal structure of Rad4-Rad23 bound to a UV-damaged DNA
Components
  • DNA repair protein RAD4
  • UV excision repair protein RAD23
  • damaged strand of the CPD-mismatch DNA
  • native strand of the CPD-mismatch DNA
KeywordsDNA BINDING PROTEIN/DNA / ALPHA-BETA STRUCTURE / BETA HAIRPIN / TRANSGLUTAMINASE FOLD / DNA-DAMAGE RECOGNITION / DNA REPAIR / DNA BINDING PROTEIN / NUCLEOTIDE EXCISION REPAIR / XERODERMA PIGMENTOSUM / DNA BINDING / PROTEIN-DNA COMPLEX / CYCLOBUTANEPYRIMIDINE CPD DIMER / ULTRAVIOLET UV DAMAGE / MISMATCH DNA / DNA BINDING PROTEIN-DNA COMPLEX
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 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 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 / 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 / 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 Complex / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA repair protein RAD4 / UV excision repair protein RAD23
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.1 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 2.0Feb 21, 2024Group: Data collection / Database references / Polymer sequence
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code / _struct_ref_seq_dif.details
Remark 400 COMPOUND THE DAMAGED RESIDUES, LABELED NN, FORM CIS-SYN CYCLOBUTANE PYRIMIDINE DIMER AND ARE NOT ... COMPOUND THE DAMAGED RESIDUES, LABELED NN, FORM CIS-SYN CYCLOBUTANE PYRIMIDINE DIMER AND ARE NOT VISIBLE IN ELECTRON DENSITY
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
W: native strand of the CPD-mismatch DNA
Y: damaged strand of the CPD-mismatch DNA
A: DNA repair protein RAD4
X: UV excision repair protein RAD23


Theoretical massNumber of molelcules
Total (without water)94,4174
Polymers94,4174
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.644, 79.644, 403.96
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: DNA chain native strand of the CPD-mismatch DNA


Mass: 7263.716 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain damaged strand of the CPD-mismatch DNA


Mass: 7229.614 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: MODIFIED RESIDUES LABELED NN ARE NOT VISIBLE, SEE REMARK 400
#3: 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
#4: 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
Sequence detailsDNA PLASMID SEQUENCING DATA CONFIRM THE REPORTED SEQUENCE

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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: 3.39 Å3/Da / Density % sol: 63.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 50 mM bis-tris propane, 100mM sodium chloride, 6% (v/v) isopropanol, 14 mM calcium chloride and 5 mM dithiothreitol, pH 6.8, hanging-drop vapor diffusion, temperature 277K, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1bis-tris propane11
2NaCl11
3CaCl211
4isopropanol11
5dithiothreitol11
6bis-tris propane12
7NaCl12
8CaCl212
9isopropanol12
10dithiothreitol12

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97922 / Wavelength: 0.97922 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 3, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97922 Å / Relative weight: 1
ReflectionResolution: 3.1→30 Å / Num. obs: 23795

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3data extraction
RefinementResolution: 3.1→30 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.898 / SU B: 37.801 / SU ML: 0.302 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.446 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1170 5.1 %RANDOM
Rwork0.246 ---
all0.248 23084 --
obs0.248 23084 93.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 67.97 Å2
Baniso -1Baniso -2Baniso -3
1-1.74 Å20 Å20 Å2
2--1.74 Å20 Å2
3----3.48 Å2
Refinement stepCycle: LAST / Resolution: 3.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4548 932 0 0 5480
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0225686
X-RAY DIFFRACTIONr_angle_refined_deg1.2412.1747855
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3215553
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.59623.056216
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.82415891
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5481543
X-RAY DIFFRACTIONr_chiral_restr0.0710.2858
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023934
X-RAY DIFFRACTIONr_nbd_refined0.2150.22614
X-RAY DIFFRACTIONr_nbtor_refined0.3120.23754
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2164
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.29
X-RAY DIFFRACTIONr_mcbond_it0.7591.252826
X-RAY DIFFRACTIONr_mcangle_it1.3091.754502
X-RAY DIFFRACTIONr_scbond_it1.29123534
X-RAY DIFFRACTIONr_scangle_it2.09133353
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 73 -
Rwork0.295 1485 -
all-1558 -
obs--87.73 %

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