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- PDB-6ubf: Role of Beta-hairpin motifs in the DNA duplex opening by the Rad4... -

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Basic information

Entry
Database: PDB / ID: 6ubf
TitleRole of Beta-hairpin motifs in the DNA duplex opening by the Rad4/XPC nucleotide excision repair complex
Components
  • DNA (5'-D(*AP*TP*TP*GP*TP*AP*GP*CP*GP*GP*GP*AP*TP*GP*TP*CP*GP*AP*GP*TP*CP*A)-3')
  • DNA (5'-D(*TP*TP*GP*AP*CP*TP*CP*(G47)P*AP*CP*AP*TP*CP*CP*C*GP*CP*TP*AP*CP*AP*A)-3')
  • DNA repair protein RAD4
  • UV excision repair protein RAD23
KeywordsDNA BINDING PROTEIN/DNA / DNA damage repair / Beta hairpin motif / chemical crosslinking / 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
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 ...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 / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / Transglutaminase-like superfamily / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Papain-like cysteine peptidase superfamily / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
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 / MOLECULAR REPLACEMENT / Resolution: 4.597 Å
AuthorsPaul, D. / Min, J.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1412692 United States
CitationJournal: Nat Commun / Year: 2015
Title: Kinetic gating mechanism of DNA damage recognition by Rad4/XPC.
Authors: Chen, X. / Velmurugu, Y. / Zheng, G. / Park, B. / Shim, Y. / Kim, Y. / Liu, L. / Van Houten, B. / He, C. / Ansari, A. / Min, J.H.
History
DepositionSep 11, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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 (5'-D(*TP*TP*GP*AP*CP*TP*CP*(G47)P*AP*CP*AP*TP*CP*CP*C*GP*CP*TP*AP*CP*AP*A)-3')
Y: DNA (5'-D(*AP*TP*TP*GP*TP*AP*GP*CP*GP*GP*GP*AP*TP*GP*TP*CP*GP*AP*GP*TP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)94,4134
Polymers94,4134
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7730 Å2
ΔGint-49 kcal/mol
Surface area35050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.723, 78.723, 403.824
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: Protein DNA repair protein RAD4


Mass: 61828.648 Da / Num. of mol.: 1 / Fragment: UNP residues 101-632
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RAD23, YEL037C, SYGP-ORF29 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P32628
#3: DNA chain DNA (5'-D(*TP*TP*GP*AP*CP*TP*CP*(G47)P*AP*CP*AP*TP*CP*CP*C*GP*CP*TP*AP*CP*AP*A)-3')


Mass: 7294.800 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)
#4: DNA chain DNA (5'-D(*AP*TP*TP*GP*TP*AP*GP*CP*GP*GP*GP*AP*TP*GP*TP*CP*GP*AP*GP*TP*CP*A)-3')


Mass: 7505.837 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)
Has ligand of interestN

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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: 62.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 50 mM BTP-HCl, 150 mM sodium chloride, 12% isopropanol

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Data collection

DiffractionMean temperature: 277 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-E / Wavelength: 0.97919 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 4→50 Å / Num. obs: 7782 / % possible obs: 100 % / Redundancy: 13.7 % / Biso Wilson estimate: 198.43 Å2 / Rmerge(I) obs: 0.267 / Rpim(I) all: 0.079 / Rrim(I) all: 0.279 / Χ2: 14.454 / Net I/σ(I): 5 / Num. measured all: 166159
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
4-4.0711.15600.8580.3460.768100
4.07-4.1411.85990.9420.2710.72999.70.9260.966
4.14-4.2213.25800.8870.2560.7681000.9320.968
4.22-4.3113.55840.9090.220.8351000.8060.836
4.31-4.413.75900.9470.170.8361000.6280.651
4.4-4.513.85890.9640.1390.961000.5130.532
4.5-4.6213.95880.9540.1331.1021000.490.508
4.62-4.7413.75960.9810.1081.0911000.3970.412
4.74-4.8813.95860.9810.1011.1971000.3730.387
4.88-5.0413.86020.9880.0841.2391000.3120.323
5.04-5.2213.95970.9820.0831.5011000.3070.318
5.22-5.4314.15820.9760.0841.5431000.3110.323
5.43-5.6713.86270.9760.081.8731000.2910.302
5.67-5.9714.45950.9690.0791.9341000.2920.303
5.97-6.3514.36090.9820.0662.1061000.2460.255
6.35-6.8414.86130.8360.0614.0551000.220.228
6.84-7.5214.96200.9690.0535.8651000.2020.209
7.52-8.614.86340.9920.0413.16999.80.1540.16
8.6-10.8213.96430.9840.0431.28599.70.1430.149
10.82-5012.57430.7310.0980.3161000.6950.332

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4YIR

4yir


Resolution: 4.597→48.747 Å / SU ML: 0.66 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 45.74
RfactorNum. reflection% reflection
Rfree0.3558 305 4.64 %
Rwork0.3144 --
obs0.316 6576 84.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 442.73 Å2 / Biso mean: 279.9875 Å2 / Biso min: 208.59 Å2
Refinement stepCycle: final / Resolution: 4.597→48.747 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4355 879 0 0 5234
Num. residues----576
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095428
X-RAY DIFFRACTIONf_angle_d1.4157490
X-RAY DIFFRACTIONf_chiral_restr0.082818
X-RAY DIFFRACTIONf_plane_restr0.009801
X-RAY DIFFRACTIONf_dihedral_angle_d16.2013140
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
4.6-5.78970.41371320.3983244168
5.7897-48.740.3411730.29613830100

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