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- PDB-6cfi: Crystal structure of Rad4-Rad23 bound to a 6-4 photoproduct UV lesion -

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Basic information

Entry
Database: PDB / ID: 6cfi
TitleCrystal structure of Rad4-Rad23 bound to a 6-4 photoproduct UV lesion
Components
  • DNA (5'-D(*AP*TP*TP*GP*TP*AP*GP*CP*(T64)P*TP*GP*GP*AP*TP*GP*TP*TP*GP*AP*GP*TP*CP*A)-3')
  • DNA repair protein RAD4
  • DNA('-D(*TP*TP*GP*AP*CP*TP*CP*AP*AP*CP*AP*TP*CP*CP*AP*AP*AP*GP*CP*TP*AP*CP*AP*A)-')
  • UV excision repair protein RAD23
KeywordsDNA BINDING PROTEIN/DNA / nucleotide excision repair / DNA damage repair / xeroderma pigmentosum / Ultraviolet / XPC / 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 / ubiquitin-dependent glycoprotein ERAD pathway / XPC complex / nucleotide-excision repair, DNA damage recognition / SUMOylation of DNA damage response and repair proteins / protein deglycosylation / proteasome binding / DNA topological change ...PNGase complex / nucleotide-excision repair factor 2 complex / single-strand break-containing DNA binding / ubiquitin-dependent glycoprotein ERAD pathway / XPC complex / nucleotide-excision repair, DNA damage recognition / SUMOylation of DNA damage response and repair proteins / protein deglycosylation / proteasome binding / DNA topological change / polyubiquitin modification-dependent protein binding / mismatch repair / : / ubiquitin binding / nucleotide-excision repair / protein-macromolecule adaptor activity / single-stranded DNA binding / 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 / Coagulation Factor XIII; Chain A, domain 2 / Transglutaminase-like / 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 BHD1 / Rad4, beta-hairpin domain BHD2 / XPC-binding domain / Coagulation Factor XIII; Chain A, domain 2 / Transglutaminase-like / 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 / 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-like domain / Ubiquitin domain profile. / 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 S288c (yeast)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.36241919841 Å
AuthorsMin, J. / Jeffrey, P.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1412692 United States
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Structure and mechanism of pyrimidine-pyrimidone (6-4) photoproduct recognition by the Rad4/XPC nucleotide excision repair complex.
Authors: Paul, D. / Mu, H. / Zhao, H. / Ouerfelli, O. / Jeffrey, P.D. / Broyde, S. / Min, J.H.
History
DepositionFeb 15, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2May 26, 2021Group: Database references / Structure summary / Category: chem_comp / citation / citation_author
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
W: DNA('-D(*TP*TP*GP*AP*CP*TP*CP*AP*AP*CP*AP*TP*CP*CP*AP*AP*AP*GP*CP*TP*AP*CP*AP*A)-')
Y: DNA (5'-D(*AP*TP*TP*GP*TP*AP*GP*CP*(T64)P*TP*GP*GP*AP*TP*GP*TP*TP*GP*AP*GP*TP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)95,1204
Polymers95,1204
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8110 Å2
ΔGint-38 kcal/mol
Surface area35920 Å2
Unit cell
Length a, b, c (Å)80.201, 80.201, 405.025
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein DNA repair protein RAD4 /


Mass: 62600.555 Da / Num. of mol.: 1 / Fragment: residues 101-632
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Gene: RAD4, YER162C / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P14736
#2: Protein UV excision repair protein RAD23


Mass: 17783.352 Da / Num. of mol.: 1 / Fragment: residues 230-398
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Gene: RAD23, YEL037C, SYGP-ORF29 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P32628
#3: DNA chain DNA('-D(*TP*TP*GP*AP*CP*TP*CP*AP*AP*CP*AP*TP*CP*CP*AP*AP*AP*GP*CP*TP*AP*CP*AP*A)-')


Mass: 7290.759 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(*AP*TP*TP*GP*TP*AP*GP*CP*(T64)P*TP*GP*GP*AP*TP*GP*TP*TP*GP*AP*GP*TP*CP*A)-3')


Mass: 7445.811 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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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: 4.13 Å3/Da / Density % sol: 70.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: bis-tris propane 5 mM sodium chloride 100 mM 1-propanol 14% spermidine-HCl 5 mM dithiothreitol 5 mM

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 18-ID / Wavelength: 0.97938 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Oct 28, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97938 Å / Relative weight: 1
ReflectionResolution: 3.362→68.95 Å / Num. obs: 19112 / % possible obs: 95.89 % / Redundancy: 13.8 % / Biso Wilson estimate: 100.86313439 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.232 / Rpim(I) all: 0.06416 / Rrim(I) all: 0.2411 / Net I/σ(I): 11.98
Reflection shellResolution: 3.362→3.483 Å / Redundancy: 8.2 % / Num. unique obs: 1407 / % possible all: 72.75

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Processing

Software
NameVersionClassification
PHENIX1.12rc1_2801refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.36241919841→74.5664038231 Å / SU ML: 0.541770523749 / Cross valid method: FREE R-VALUE / σ(F): 1.99257533985 / Phase error: 27.3113264241
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.26822142011 964 5.04474331467 %
Rwork0.218896046274 18145 -
obs0.221283344424 19109 95.904642409 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 113.091042262 Å2
Refinement stepCycle: LAST / Resolution: 3.36241919841→74.5664038231 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4495 978 0 0 5473
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005274048039425687
X-RAY DIFFRACTIONf_angle_d0.9104467484987871
X-RAY DIFFRACTIONf_chiral_restr0.0469385679943858
X-RAY DIFFRACTIONf_plane_restr0.00747620322038831
X-RAY DIFFRACTIONf_dihedral_angle_d19.11107732313278
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3624-3.53970.3966575359731060.331894378762032X-RAY DIFFRACTION77.2957339118
3.5397-3.76150.3564459692161330.2969614879752442X-RAY DIFFRACTION93.3647570703
3.7615-4.05190.3138700830031740.24665715282618X-RAY DIFFRACTION100
4.0519-4.45960.2436453831241610.1949014278852650X-RAY DIFFRACTION100
4.4596-5.10480.2249110148091140.178826935652701X-RAY DIFFRACTION100
5.1048-6.43090.2573238854441350.2210062599952748X-RAY DIFFRACTION100
6.4309-74.58470.2412331578861410.201939499092954X-RAY DIFFRACTION99.8709261052

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