6UBF: DNA repair protein RAD4

Role of Beta-hairpin motifs in the DNA duplex opening by the Rad4/XPC nucleotide excision repair complex. Determined by X-ray diffraction at 4.6 Å resolution. Released 14 Oct 2020.

Method
X-ray diffraction
Resolution
4.6 Å
Organism
Saccharomyces cerevisiae
Chains
4
Atoms
5,234
Mol. weight
94.41 kDa
Released
14 Oct 2020

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

Secondary structure: helices and β-sheets

6UBF contains 34 α-helices and 23 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: 29 helices, 23 β-strands

ElementResiduesLengthSheet
α-helix134-16330
α-helix165-1728
α-helix177-1837
α-helix185-1873
α-helix192-21322
β-strand216-21721
α-helix219-2202
α-helix230-2367
α-helix247-25711
β-strand259-26021
α-helix262-27514
β-strand280-28672
α-helix288-2903
α-helix305-3095
β-strand315-32172
β-strand326-33162
β-strand337-33932
β-strand362-36652
β-strand372-37432
α-helix376-3794
α-helix387-3904
α-helix392-3943
α-helix396-40914
α-helix416-43116
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-strand490-49125
α-helix493-4975
β-strand501-50336
β-strand51517
β-strand52717
α-helix528-5303
β-strand532-53325
α-helix534-5363
β-strand537-53936
α-helix542-5454
β-strand559-56028
α-helix564-5663
β-strand571-57558
α-helix579-5868
β-strand592-59438
β-strand609-61578
α-helix616-6183
α-helix619-6279
α-helix629-6313
Chain X: 5 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix260-27112
α-helix273-2753
α-helix276-28611
α-helix290-2967
α-helix298-30710

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
DNA repair protein RAD4Aprotein531Saccharomyces cerevisiaeP14736 (AlphaFold model)
UV excision repair protein RAD23Xprotein171Saccharomyces cerevisiaeP32628 (AlphaFold model)
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')WDNA24Saccharomyces cerevisiae
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')YDNA24Saccharomyces cerevisiae
Sequence of entity 1 (A), FASTA
>6UBF_1 DNA repair protein RAD4 (chains A)
GSSRAMGNEVAGVEDISVEITPSSKRNSDARRTSRNCSSNEERKRRKYFHMLYLVCLMVH
GFIRNEWINSKRLSRKLSNLVPEKVFELLHPQKDEELPLRSTRKLLDGLKKCMELWQKHW
KITKKYDNEGLYMRTWKEIEMSANNKRKFKTLKRSDFLRAVSKGHGDPDISVQGFVAMLR
ACNVNARLIMSCQPPDFTNMKIDTSLNGNNAYKDMVKYPIFWCEVWDKFSKKWITVDPVN
LKTIEQVRLHSKLAPKGVACCERNMLRYVIAYDRKYGCRDVTRRYAQWMNSKVRKRRITK
DDFGEKWFRKVITALHHRKRTKIDDYEDQYFFRRDESEGIPDSVQDLKNHPYYVLEQDIK
QTQIVKPGCKECGYLKVHGKVGKVLKVYAKRDIADLKSARQWYMNGRILKTGSRCKKVIK
RTVGRPKGEAEEEDERLYSFEDTELYIPPLASASGEITKNTFGNIEVFAPTMIPGNCCLV
ENPVAIKAARFLGVEFAPAVTSFKFPVLSGIVVAKWLREAIETAIDGIEFI
Sequence of entity 2 (X), FASTA
>6UBF_2 UV excision repair protein RAD23 (chains X)
GSGNASSGALGTTGGATDAAQGGPPGSIGLTVEDLLSLRQVVSGNPEALAPLLENISARY
PQLREHIMANPEVFVSMLLEAVGDNMQDVMEGADDMVEGEDIEVTGEAAAAGLGQGEGEG
SFQVDYTPEDDQAISRLCELGFERDLVIQVYFACDKNEEAAANILFSDHAD
Sequence of entity 3 (W), FASTA
>6UBF_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') (chains W)
TTGACTCGACATCCCCCGCTACAA
Sequence of entity 4 (Y), FASTA
>6UBF_4 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') (chains Y)
ATTGTAGCGGGGGATGTCGAGTCA

Primary citation

Kinetic gating mechanism of DNA damage recognition by Rad4/XPC. Chen, X., Velmurugu, Y., Zheng, G. et al. Nat Commun (2015) 6:5849. DOI 10.1038/ncomms6849 · 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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