6UG1: DNA repair protein RAD4

Sequence impact in DNA duplex opening by the Rad4/XPC nucleotide excision repair complex. Determined by X-ray diffraction at 2.83 Å resolution. Released 31 Mar 2021.

Method
X-ray diffraction
Resolution
2.83 Å
Organisms
Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Saccharomyces cerevisiae
Chains
4
Atoms
5,231
Mol. weight
78.12 kDa
Released
31 Mar 2021

Explore 6UG1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6UG1 contains 32 α-helices and 22 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 27 helices, 22 β-strands

ElementResiduesLengthSheet
α-helix134-16229
α-helix165-1728
α-helix177-1837
α-helix185-1873
α-helix192-21322
β-strand216-21721
α-helix219-2202
α-helix230-2389
α-helix247-25711
β-strand259-26021
α-helix262-27514
β-strand280-28672
α-helix288-2903
α-helix306-3094
β-strand315-32172
β-strand326-33162
β-strand337-33932
α-helix354-3563
β-strand362-36652
β-strand372-37432
α-helix376-3794
α-helix387-3904
α-helix392-3943
α-helix396-40914
α-helix416-43015
α-helix439-4413
β-strand447-44933
α-helix450-4523
β-strand457-45934
α-helix4601
β-strand467-47043
β-strand478-48363
α-helix484-4863
β-strand487-48934
β-strand490-49235
α-helix493-4975
β-strand501-50336
β-strand511-51225
β-strand530-53345
α-helix534-5363
β-strand537-53936
β-strand559-56027
α-helix564-5663
β-strand571-57557
α-helix579-5857
β-strand592-59437
β-strand609-61577
α-helix619-6279
α-helix629-6313
Chain X: 5 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix259-27113
α-helix273-2753
α-helix276-28611
α-helix290-2967
α-helix298-3069

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
DNA repair protein RAD4Aprotein504Saccharomyces cerevisiae (strain ATCC 204508 / S288c)P14736 (AlphaFold model)
UV excision repair protein RAD23Xprotein57Saccharomyces cerevisiae (strain ATCC 204508 / S288c)P32628 (AlphaFold model)
DNA (5'-d(*ap*tp*tp*gp*tp*ap*gp*gp*gp*ap*tp*gp*tp*cp*gp*ap*gp*tp*cp*a)-3')YDNA21Saccharomyces cerevisiae
DNA (5'-D(*TP*TP*GP*AP*CP*TP*CP*(G47)P*AP*CP*AP*TP*CP*CP*CP*CP*TP*AP*CP*AP*A)-3')WDNA21Saccharomyces cerevisiae
Sequence of entity 1 (A), FASTA
>6UG1_1 DNA repair protein RAD4 (chains A)
RNCSSNEERKRRKYFHMLYLVCLMVHGFIRNEWINSKRLSRKLSNLVPEKVFELLHPQKD
EELPLRSTRKLLDGLKKCMELWQKHWKITKKYDNEGLYMRTWKEIEMSANNKRKFKTLKR
SDFLRAVSKGHGDPDISVQGFVAMLRACNVNARLIMSCQPPDFTNMKIDTSLNGNNAYKD
MVKYPIFWCEVWDKFSKKWITVDPVNLKTIEQVRLHSKLAPKGVACCERNMLRYVIAYDR
KYGCRDVTRRYAQWMNSKVRKRRITKDDFGEKWFRKVITALHHRKRTKIDDYEDQYFFRR
DESEGIPDSVQDLKNHPYYVLEQDIKQTQIVKPGCKECGYLKVHGKVGKVLKVYAKRDIA
DLKSARQWYMNGRILKTGSRCKKVIKRTVGRPKGEAEEDAERLYSFEDTELYIPPLASAS
GEITKNTFGNIEVFAPTMIPGNCCLVENPVAIKAARFLGVEFAPAVTSFKFERGSTVKPV
LSGIVVAKWLREAIETAIDGIEFI
Sequence of entity 2 (X), FASTA
>6UG1_2 UV excision repair protein RAD23 (chains X)
AGLTVEDLLSLRQVVSGNPEALAPLLENISARYPQLREHIMANPEVFVSMLLEAVGD
Sequence of entity 3 (Y), FASTA
>6UG1_3 DNA (5'-D(*AP*TP*TP*GP*TP*AP*GP*GP*GP*AP*TP*GP*TP*CP*GP*AP*GP*TP*CP*A)-3') (chains Y)
GTAGCGCGCGATGTCGAGTCA
Sequence of entity 4 (W), FASTA
>6UG1_4 DNA (5'-D(*TP*TP*GP*AP*CP*TP*CP*(G47)P*AP*CP*AP*TP*CP*CP*CP*CP*TP*AP*CP*AP*A)-3') (chains W)
TGACTCGACATCGCGCGCTAC

Primary citation

Impact of DNA sequences on DNA 'opening' by the Rad4/XPC nucleotide excision repair complex. Paul, D., Mu, H., Tavakoli, A. et al. DNA Repair (Amst) (2021) 107:103194-103194. DOI 10.1016/j.dnarep.2021.103194 · PubMed

Other PDB entries of the same protein (UniProt P14736 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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