4YIR: Rad4-Rad23 crosslinked to an undamaged DNA

Crystal structure of Rad4-Rad23 crosslinked to an undamaged DNA. Determined by X-ray diffraction at 3.05 Å resolution. Released 11 Mar 2015.

Method: X-ray diffraction
Resolution: 3.05 Å
Organisms: Saccharomyces cerevisiae (strain ATCC 204508 / S288c), synthetic construct
Chains: 4
Atoms: 5,459
Mol. weight: 95.17 kDa
Released: 11 Mar 2015

Explore 4YIR in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4YIR contains 36 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: 31 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	134-163	30
α-helix	165-172	8
α-helix	177-182	6
α-helix	185-187	3
α-helix	192-213	22
β-strand	216-217	2	1
α-helix	219-220	2
α-helix	230-236	7
α-helix	247-257	11
β-strand	259-260	2	1
α-helix	262-275	14
β-strand	280-286	7	2
α-helix	288-290	3
α-helix	305-309	5
β-strand	315-321	7	2
β-strand	326-331	6	2
β-strand	337-339	3	2
α-helix	354-357	4
β-strand	362-366	5	2
β-strand	372-374	3	2
α-helix	376-379	4
α-helix	387-390	4
α-helix	392-394	3
α-helix	396-409	14
α-helix	416-430	15
α-helix	438-441	4
β-strand	447-449	3	3
α-helix	450-452	3
β-strand	457-459	3	4
α-helix	460	1
β-strand	467-470	4	3
β-strand	478-483	6	3
α-helix	484-486	3
β-strand	487-489	3	4
β-strand	491-492	2	5
α-helix	493-497	5
β-strand	501-503	3	6
α-helix	504	1
α-helix	507-509	3
β-strand	511-515	5	5
β-strand	527-532	6	5
α-helix	534-536	3
β-strand	537-539	3	6
α-helix	542-545	4
β-strand	559-560	2	7
α-helix	564-566	3
β-strand	571-575	5	7
α-helix	579-586	8
β-strand	592-599	8	7
β-strand	605-615	11	7
α-helix	616-618	3
α-helix	619-627	9
α-helix	629-631	3

Chain X: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	260-271	12
α-helix	273-275	3
α-helix	276-286	11
α-helix	290-296	7
α-helix	298-307	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA repair protein RAD4	A	protein	538	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P14736 (AlphaFold model)
UV excision repair protein RAD23	X	protein	171	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P32628 (AlphaFold model)
DNA (5'-D(TPTPGPAPCPTPCP(G47)PAPCPAPTPCPCPCPCPCPGPCPTPAPCPAPA)-3')	W	DNA	24	synthetic construct
DNA (5'-d(aptptpgptpapgpcpggpgpgpaptpgptpcpgpapgptpcp*a)-3')	Y	DNA	24	synthetic construct

Sequence of entity 1 (A), FASTA

>4YIR_1 DNA repair protein RAD4 (chains A)
GSSRAMGNEVAGVEDISVEITPSSKRNSDARRTSRNCSSNEERKRRKYFHMLYLVCLMVH
GFIRNEWINSKRLSRKLSNLVPEKVFELLHPQKDEELPLRSTRKLLDGLKKCMELWQKHW
KITKKYDNEGLYMRTWKEIEMSANNKRKFKTLKRSDFLRAVSKGHGDPDISVQGFVAMLR
ACNVNARLIMSCQPPDFTNMKIDTSLNGNNAYKDMVKYPIFWCEVWDKFSKKWITVDPVN
LKTIEQVRLHSKLAPKGVACCERNMLRYVIAYDRKYGCRDVTRRYAQWMNSKVRKRRITK
DDFGEKWFRKVITALHHRKRTKIDDYEDQYFFRRDESEGIPDSVQDLKNHPYYVLEQDIK
QTQIVKPGCKECGYLKVHGKVGKVLKVYAKRDIADLKSARQWYMNGRILKTGSRCKKVIK
RTVGRPKGEAEEEDERLYSFEDTELYIPPLASASGEITKNTFGNIEVFAPTMIPGNCCLV
ENPVAIKAARFLGVEFAPAVTSFKFERGSTVKPVLSGIVVAKWLREAIETAIDGIEFI

Sequence of entity 2 (X), FASTA

>4YIR_2 UV excision repair protein RAD23 (chains X)
GSGNASSGALGTTGGATDAAQGGPPGSIGLTVEDLLSLRQVVSGNPEALAPLLENISARY
PQLREHIMANPEVFVSMLLEAVGDNMQDVMEGADDMVEGEDIEVTGEAAAAGLGQGEGEG
SFQVDYTPEDDQAISRLCELGFERDLVIQVYFACDKNEEAAANILFSDHAD

Sequence of entity 3 (W), FASTA

>4YIR_3 DNA (5'-D(*TP*TP*GP*AP*CP*TP*CP*(G47)P*AP*CP*AP*TP*CP*CP*CP*CP*CP*GP*CP*TP*AP*CP*AP*A)-3') (chains W)
TTGACTCGACATCCCCCGCTACAA

Sequence of entity 4 (Y), FASTA

>4YIR_4 DNA (5'-D(*AP*TP*TP*GP*TP*AP*GP*CP*G*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:

2QSF 2.35 Å, Crystal structure of the Rad4-Rad23 complex
2QSH 2.81 Å, Crystal structure of Rad4-Rad23 bound to a mismatch DNA
6UG1 2.83 Å, Sequence impact in DNA duplex opening by the Rad4/XPC nucleotide excision repair complex
2QSG 3.1 Å, Crystal structure of Rad4-Rad23 bound to a UV-damaged DNA
6UIN 3.35 Å, Role of Beta-hairpin motifs in the DNA duplex opening by the Rad4/XPC nucleotide…
6CFI 3.36 Å, Crystal structure of Rad4-Rad23 bound to a 6-4 photoproduct UV lesion
6UBF 4.6 Å, Role of Beta-hairpin motifs in the DNA duplex opening by the Rad4/XPC nucleotide…
7M2U 8.2 Å, Nucleotide Excision Repair complex TFIIH Rad4-33
7K04 9.25 Å, Structure of TFIIH/Rad4-Rad23-Rad33/DNA in DNA opening
2M14 NMR structure of the complex between the PH domain of the Tfb1 subunit from TFIIH and Rad4

Browse structure collections

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