SNAP output for PDB entry 7k04 [SNAP web server]

PDB-id

7k04; SNAP-derived features in text and JSON formats; DNAproDB

Class

nuclear protein-DNA

Method

cryo-EM (9.25 Å)

Summary

Structure of tfiih-rad4-rad23-rad33-DNA in DNA opening

Reference

van Eeuwen T, Shim Y, Kim HJ, Zhao T, Basu S, Garcia BA, Kaplan CD, Min JH, Murakami K (2021): "Cryo-EM structure of TFIIH/Rad4-Rad23-Rad33 in damaged DNA opening in nucleotide excision repair." Nat Commun, 12, 3338. doi: 10.1038/s41467-021-23684-x.

Abstract

The versatile nucleotide excision repair (NER) pathway initiates as the XPC-RAD23B-CETN2 complex first recognizes DNA lesions from the genomic DNA and recruits the general transcription factor complex, TFIIH, for subsequent lesion verification. Here, we present a cryo-EM structure of an NER initiation complex containing Rad4-Rad23-Rad33 (yeast homologue of XPC-RAD23B-CETN2) and 7-subunit coreTFIIH assembled on a carcinogen-DNA adduct lesion at 3.9-9.2 Å resolution. A ~30-bp DNA duplex could be mapped as it straddles between Rad4 and the Ssl2 (XPB) subunit of TFIIH on the 3' and 5' side of the lesion, respectively. The simultaneous binding with Rad4 and TFIIH was permitted by an unwinding of DNA at the lesion. Translocation coupled with torque generation by Ssl2 and Rad4 would extend the DNA unwinding at the lesion and deliver the damaged strand to Rad3 (XPD) in an open form suitable for subsequent lesion scanning and verification.