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

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Basic information

Entry
Database: PDB / ID: 6uin
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*NP*NP*NP*NP*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*CP*CP*CP*CP*CP*TP*AP*CP*AP*A)-3')
  • DNA repair protein RAD4
  • UV excision repair protein RAD23
KeywordsDNA BINDING PROTEIN/DNA / DNA damage recognition / DNA damage repair / nucleotide excision repair / Beta-hairpin motif / xeroderma pigmentosum / XPC / Rad4 / molecular dynamics simulations / 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 / protein deglycosylation / proteasome binding / DNA topological change / polyubiquitin modification-dependent protein binding ...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 / protein deglycosylation / proteasome binding / DNA topological change / polyubiquitin modification-dependent protein binding / mismatch repair / ERAD pathway / 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 / cytoplasm / cytosol
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: 3.348 Å
AuthorsPaul, D. / Min, J.-H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
Citation
Journal: Nucleic Acids Res. / Year: 2021
Title: Tethering-facilitated DNA 'opening' and complementary roles of beta-hairpin motifs in the Rad4/XPC DNA damage sensor protein
Authors: Paul, D. / Mu, H. / Tavakoli, A. / Dai, Q. / Chen, X. / Chakraborty, S. / He, C. / Ansari, A. / Broyde, S. / Min, J.H.
#1: Journal: 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
DepositionOct 1, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.id ..._citation.country / _citation.id / _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 1.2Oct 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*CP*CP*CP*CP*CP*TP*AP*CP*AP*A)-3')
Y: DNA (5'-D(*AP*TP*TP*GP*TP*AP*GP*NP*NP*NP*NP*GP*GP*AP*TP*GP*TP*CP*GP*AP*GP*TP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)94,6114
Polymers94,6114
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7180 Å2
ΔGint-48 kcal/mol
Surface area34050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.665, 77.665, 264.054
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein DNA repair protein RAD4


Mass: 62559.445 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 / Fragment: UNP residues 230-398
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*CP*CP*CP*CP*CP*TP*AP*CP*AP*A)-3')


Mass: 7254.775 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*NP*NP*NP*NP*GP*GP*AP*TP*GP*TP*CP*GP*AP*GP*TP*CP*A)-3')


Mass: 7013.417 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: 2.45 Å3/Da / Density % sol: 49.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 50 mM BTP-HCl, 200 mM sodium chloride, 12% isopropanol, 100 mM calcium chloride

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Data collection

DiffractionMean temperature: 277 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 1, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.34→50 Å / Num. obs: 12932 / % possible obs: 99 % / Redundancy: 6.4 % / Rsym value: 0.036 / Net I/σ(I): 19.1
Reflection shellHighest resolution: 3.34 Å

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Processing

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

4yir


Resolution: 3.348→38.833 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 30.22
RfactorNum. reflection% reflection
Rfree0.2623 1286 9.95 %
Rwork0.2087 --
obs0.2141 12925 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 332.92 Å2 / Biso mean: 148.4842 Å2 / Biso min: 76.8 Å2
Refinement stepCycle: final / Resolution: 3.348→38.833 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4342 836 0 0 5178
Num. residues----573
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095370
X-RAY DIFFRACTIONf_angle_d1.5787400
X-RAY DIFFRACTIONf_chiral_restr0.088807
X-RAY DIFFRACTIONf_plane_restr0.009794
X-RAY DIFFRACTIONf_dihedral_angle_d18.3883110
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.35-3.48190.35281400.30011298100
3.4819-3.64020.30271450.25671292100
3.6402-3.8320.32561430.2431286100
3.832-4.07180.31221480.21131302100
4.0718-4.38580.27011450.20881281100
4.3858-4.82650.22751420.18611304100
4.8265-5.52320.25551380.19491282100
5.5232-6.95210.28151360.24671300100
6.9521-38.70.23351490.1831129499

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