- EMDB-22576: TFIIH/Rad4-23-33 Complex in NER focused on Rad4-33 -
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Open data
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Basic information
Entry
Database: EMDB / ID: EMD-22576
Title
TFIIH/Rad4-23-33 Complex in NER focused on Rad4-33
Map data
Cryo-EM map of TFIIH in complex with Rad4-Rad33 on AAF DNA with focused classification on Rad4-33-Ssl2 contacts. Composite map after multibody refinement.
Sample
Complex: Ternary complex of Saccharomyces cerevisiae TFIIH, DNA damage proteins Rad4-Rad23-Rad33 and N-acetoxy-acetominofluorinated DNA.
Function / homology
Function and homology information
nucleotide-excision repair factor 2 complex / single-strand break-containing DNA binding / XPC complex / nucleotide-excision repair, DNA damage recognition / regulation of mitotic recombination / RNA polymerase II promoter clearance / phosphatidylinositol-5-phosphate binding / positive regulation of mitotic recombination / nucleotide-excision repair factor 3 complex / nucleotide-excision repair, preincision complex assembly ...nucleotide-excision repair factor 2 complex / single-strand break-containing DNA binding / XPC complex / nucleotide-excision repair, DNA damage recognition / regulation of mitotic recombination / RNA polymerase II promoter clearance / phosphatidylinositol-5-phosphate binding / positive regulation of mitotic recombination / nucleotide-excision repair factor 3 complex / nucleotide-excision repair, preincision complex assembly / DNA translocase activity / transcription open complex formation at RNA polymerase II promoter / phosphatidylinositol-3-phosphate binding / DNA 3'-5' helicase / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / transcription preinitiation complex / DNA duplex unwinding / poly(A)+ mRNA export from nucleus / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase II Pre-transcription Events / Formation of TC-NER Pre-Incision Complex / RNA Polymerase I Promoter Escape / 3'-5' DNA helicase activity / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription by RNA polymerase I / DNA topological change / ATPase activator activity / Dual incision in TC-NER / ATP-dependent activity, acting on DNA / mismatch repair / DNA helicase activity / nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / ubiquitin protein ligase activity / single-stranded DNA binding / 4 iron, 4 sulfur cluster binding / 5'-3' DNA helicase activity / double-stranded DNA binding / proteasome-mediated ubiquitin-dependent protein catabolic process / DNA helicase / transcription by RNA polymerase II / damaged DNA binding / DNA repair / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / zinc ion binding / ATP binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function
General transcription and DNA repair factor IIH helicase subunit XPD / DNA repair protein RAD4 / General transcription and DNA repair factor IIH subunit TFB1 / General transcription and DNA repair factor IIH helicase/translocase subunit XPB/SSL2 / General transcription and DNA repair factor IIH subunit TFB2 / DNA repair protein RAD33 / General transcription and DNA repair factor IIH subunit SSL1 / General transcription and DNA repair factor IIH subunit TFB4 / General transcription and DNA repair factor IIH subunit TFB5 Similarity search - Component
Biological species
Saccharomyces cerevisiae (brewer's yeast)
Method
single particle reconstruction / cryo EM / Resolution: 8.0 Å
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
R01-GM123233
United States
Citation
Journal: Nat Commun / Year: 2021 Title: Cryo-EM structure of TFIIH/Rad4-Rad23-Rad33 in damaged DNA opening in nucleotide excision repair. Authors: Trevor van Eeuwen / Yoonjung Shim / Hee Jong Kim / Tingting Zhao / Shrabani Basu / Benjamin A Garcia / Craig D Kaplan / Jung-Hyun Min / Kenji Murakami / 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 ...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.
History
Deposition
Sep 2, 2020
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Header (metadata) release
Jul 28, 2021
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Map release
Jul 28, 2021
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Update
Jul 28, 2021
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Current status
Jul 28, 2021
Processing site: RCSB / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Download / File: emd_22576.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation
Cryo-EM map of TFIIH in complex with Rad4-Rad33 on AAF DNA with focused classification on Rad4-33-Ssl2 contacts. Composite map after multibody refinement.
Voxel size
X=Y=Z: 1.08 Å
Density
Contour Level
By AUTHOR: 0.00239 / Movie #1: 0.00239
Minimum - Maximum
-0.0019033871 - 0.0066725626
Average (Standard dev.)
-1.4589203e-05 (±0.00044120074)
Symmetry
Space group: 1
Details
EMDB XML:
Map geometry
Axis order
X
Y
Z
Origin
0
0
0
Dimensions
300
300
300
Spacing
300
300
300
Cell
A=B=C: 324.0 Å α=β=γ: 90.0 °
CCP4 map header:
mode
Image stored as Reals
Å/pix. X/Y/Z
1.08
1.08
1.08
M x/y/z
300
300
300
origin x/y/z
0.000
0.000
0.000
length x/y/z
324.000
324.000
324.000
α/β/γ
90.000
90.000
90.000
start NX/NY/NZ
133
131
0
NX/NY/NZ
223
226
424
MAP C/R/S
1
2
3
start NC/NR/NS
0
0
0
NC/NR/NS
300
300
300
D min/max/mean
-0.002
0.007
-0.000
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Supplemental data
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Additional map: Cryo-EM map of TFIIH in complex with Rad4-Rad33...
Cryo-EM map of TFIIH in complex with Rad4-Rad33 on AAF DNA with focused classification on Rad4-33-Ssl2 contacts. TFIIH body from multibody refinement used for composite map making.
Cryo-EM map of TFIIH in complex with Rad4-Rad33 on AAF DNA with focused classification on Rad4-33-Ssl2 contacts. Map locally filtered to FSC=0.5 by blocre
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