- EMDB-18380: Focused map for UVSSA(VHS)-CSA-DDB1(BPA/BPC)-DDA1 -
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Basic information
Entry
Database: EMDB / ID: EMD-18380
Title
Focused map for UVSSA(VHS)-CSA-DDB1(BPA/BPC)-DDA1
Map data
Focused map of CSA-DDB1(BPA/BPC)-DDA1-UVSSA(VHS), sharpen
Sample
Complex: Ternary complex of UVSSA(VHS)-CSA-DDB1(BPA/BPC)-DDA1
Protein or peptide: DNA excision repair protein ERCC-8
Protein or peptide: DNA damage-binding protein 1
Protein or peptide: DET1- and DDB1-associated protein 1
Protein or peptide: UV-stimulated scaffold protein A
Keywords
Ubiquitin ligase DNA repair / LIGASE
Function / homology
Function and homology information
RNA polymerase inhibitor activity / regulation of transcription-coupled nucleotide-excision repair / nucleotide-excision repair complex / single strand break repair / positive regulation by virus of viral protein levels in host cell / chromatin-protein adaptor activity / double-strand break repair via classical nonhomologous end joining / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / Cul4-RING E3 ubiquitin ligase complex ...RNA polymerase inhibitor activity / regulation of transcription-coupled nucleotide-excision repair / nucleotide-excision repair complex / single strand break repair / positive regulation by virus of viral protein levels in host cell / chromatin-protein adaptor activity / double-strand break repair via classical nonhomologous end joining / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4A-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / negative regulation of reproductive process / negative regulation of developmental process / RNA polymerase II complex binding / cullin family protein binding / viral release from host cell / site of DNA damage / response to X-ray / ectopic germ cell programmed cell death / positive regulation of viral genome replication / proteasomal protein catabolic process / transcription-coupled nucleotide-excision repair / response to UV / protein autoubiquitination / positive regulation of gluconeogenesis / positive regulation of DNA repair / Recognition of DNA damage by PCNA-containing replication complex / DNA Damage Recognition in GG-NER / nucleotide-excision repair / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Formation of Incision Complex in GG-NER / regulation of circadian rhythm / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / nuclear matrix / Wnt signaling pathway / protein polyubiquitination / positive regulation of protein catabolic process / cellular response to UV / rhythmic process / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / site of double-strand break / Neddylation / chromosome / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / damaged DNA binding / proteasome-mediated ubiquitin-dependent protein catabolic process / response to oxidative stress / chromosome, telomeric region / protein ubiquitination / DNA repair / apoptotic process / DNA damage response / negative regulation of apoptotic process / protein-containing complex binding / nucleolus / protein-containing complex / extracellular space / DNA binding / extracellular exosome / nucleoplasm / nucleus / cytoplasm Similarity search - Function
UV-stimulated scaffold protein A / : / : / Uncharacterized conserved protein (DUF2043) / UVSSA N-terminal domain / Zinc finger UVSSA-type profile. / DET1- and DDB1-associated protein 1, N-terminal / DET1- and DDB1-associated protein 1 / Det1 complexing ubiquitin ligase / DNA excision repair protein Rad28/ERCC8/Ckn1/ATCSA-1 ...UV-stimulated scaffold protein A / : / : / Uncharacterized conserved protein (DUF2043) / UVSSA N-terminal domain / Zinc finger UVSSA-type profile. / DET1- and DDB1-associated protein 1, N-terminal / DET1- and DDB1-associated protein 1 / Det1 complexing ubiquitin ligase / DNA excision repair protein Rad28/ERCC8/Ckn1/ATCSA-1 / ENTH/VHS / RSE1/DDB1/CPSF1 second beta-propeller / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / : / CPSF A subunit region / RSE1/DDB1/CPSF1 first beta-propeller / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily Similarity search - Domain/homology
DNA excision repair protein ERCC-8 / DNA damage-binding protein 1 / UV-stimulated scaffold protein A / DET1- and DDB1-associated protein 1 Similarity search - Component
Biological species
Homo sapiens (human)
Method
single particle reconstruction / cryo EM / Resolution: 3.7 Å
Netherlands Organisation for Scientific Research (NWO)
TOP 714.017.003
Netherlands
European Molecular Biology Organization (EMBO)
ALTF 1159-2019
European Union
Citation
Journal: Nat Commun / Year: 2024 Title: The small CRL4 ubiquitin ligase component DDA1 regulates transcription-coupled repair dynamics. Authors: Diana A Llerena Schiffmacher / Shun-Hsiao Lee / Katarzyna W Kliza / Arjan F Theil / Masaki Akita / Angela Helfricht / Karel Bezstarosti / Camila Gonzalo-Hansen / Haico van Attikum / Matty ...Authors: Diana A Llerena Schiffmacher / Shun-Hsiao Lee / Katarzyna W Kliza / Arjan F Theil / Masaki Akita / Angela Helfricht / Karel Bezstarosti / Camila Gonzalo-Hansen / Haico van Attikum / Matty Verlaan-de Vries / Alfred C O Vertegaal / Jan H J Hoeijmakers / Jurgen A Marteijn / Hannes Lans / Jeroen A A Demmers / Michiel Vermeulen / Titia K Sixma / Tomoo Ogi / Wim Vermeulen / Alex Pines / Abstract: Transcription-blocking DNA lesions are specifically targeted by transcription-coupled nucleotide excision repair (TC-NER), which removes a broad spectrum of DNA lesions to preserve transcriptional ...Transcription-blocking DNA lesions are specifically targeted by transcription-coupled nucleotide excision repair (TC-NER), which removes a broad spectrum of DNA lesions to preserve transcriptional output and thereby cellular homeostasis to counteract aging. TC-NER is initiated by the stalling of RNA polymerase II at DNA lesions, which triggers the assembly of the TC-NER-specific proteins CSA, CSB and UVSSA. CSA, a WD40-repeat containing protein, is the substrate receptor subunit of a cullin-RING ubiquitin ligase complex composed of DDB1, CUL4A/B and RBX1 (CRL4). Although ubiquitination of several TC-NER proteins by CRL4 has been reported, it is still unknown how this complex is regulated. To unravel the dynamic molecular interactions and the regulation of this complex, we apply a single-step protein-complex isolation coupled to mass spectrometry analysis and identified DDA1 as a CSA interacting protein. Cryo-EM analysis shows that DDA1 is an integral component of the CRL4 complex. Functional analysis reveals that DDA1 coordinates ubiquitination dynamics during TC-NER and is required for efficient turnover and progression of this process.
Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Details: The grid was coated with graphene oxide
Vitrification
Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details
This sample was glutaraldehyde crosslinked
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Electron microscopy
Microscope
FEI TITAN KRIOS
Specialist optics
Energy filter - Slit width: 20 eV
Details
Collected on Krios 1 at Netherlands Center for Electron Nanoscopy (NeCEN)
Image recording
Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 1382 / Average electron dose: 60.0 e/Å2
Electron beam
Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
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