EMDB-15829: CRL4CSA-E2-Ub (state 2)

Basic information

Entry

Database: EMDB / ID: EMD-15829

• Title: CRL4CSA-E2-Ub (state 2)
• Map data: The main map.

Sample

• Complex: C(N)RL4CSA-E2-Ub complex.
  • Protein or peptide: Ubiquitin-conjugating enzyme E2 D2
  • Protein or peptide: NEDD8
  • Protein or peptide: E3 ubiquitin-protein ligase RBX1
  • Protein or peptide: Ubiquitin
  • Protein or peptide: DNA excision repair protein ERCC-8
  • Protein or peptide: DNA damage-binding protein 1
  • Protein or peptide: Cullin-4A
• Ligand: ZINC ION

• Keywords: DNA repair / transcription / ubiqutin / cryo-EM

Function / homology

Function:

regulation of transcription-coupled nucleotide-excision repair / nucleotide-excision repair complex / negative regulation of granulocyte differentiation / single strand break repair / (E3-independent) E2 ubiquitin-conjugating enzyme / cullin-RING-type E3 NEDD8 transferase / cellular response to chemical stress / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / positive regulation by virus of viral protein levels in host cell / regulation of DNA damage checkpoint / regulation of nucleotide-excision repair / Cul7-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / epigenetic programming in the zygotic pronuclei / double-strand break repair via classical nonhomologous end joining / spindle assembly involved in female meiosis / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / regulation of proteolysis / Cul4-RING E3 ubiquitin ligase complex / positive regulation of protein autoubiquitination / UV-damage excision repair / protein neddylation / NEDD8 ligase activity / biological process involved in interaction with symbiont / Cul5-RING ubiquitin ligase complex / negative regulation of response to oxidative stress / ubiquitin-ubiquitin ligase activity / WD40-repeat domain binding / regulation of mitotic cell cycle phase transition / Cul4A-RING E3 ubiquitin ligase complex / SCF ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / negative regulation of type I interferon production / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / E2 ubiquitin-conjugating enzyme / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Cul3-RING ubiquitin ligase complex / Prolactin receptor signaling / negative regulation of reproductive process / negative regulation of developmental process / TGF-beta receptor signaling activates SMADs / protein monoubiquitination / somatic stem cell population maintenance / ubiquitin conjugating enzyme activity / cullin family protein binding / hemopoiesis / viral release from host cell / response to X-ray / ectopic germ cell programmed cell death / proteasomal protein catabolic process / positive regulation of viral genome replication / positive regulation of G1/S transition of mitotic cell cycle / anatomical structure morphogenesis / protein autoubiquitination / transcription-coupled nucleotide-excision repair / protein K48-linked ubiquitination / Nuclear events stimulated by ALK signaling in cancer / response to UV / ubiquitin ligase complex / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / positive regulation of gluconeogenesis / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / positive regulation of TORC1 signaling / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / positive regulation of DNA repair / Downregulation of ERBB4 signaling / T cell activation / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus

Domain/homology:

DNA excision repair protein Rad28/ERCC8/Ckn1/ATCSA-1 / Nedd8-like ubiquitin / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / Cullin protein neddylation domain / Cullin, conserved site / Cullin family signature. / Cullin / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin protein neddylation domain / Cullin / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin family / Cullin family profile. / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / Mono-functional DNA-alkylating methyl methanesulfonate N-term / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / CPSF A subunit region / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / Zinc finger RING-type profile. / Zinc finger, RING-type / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / G-protein beta WD-40 repeat / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Winged helix DNA-binding domain superfamily / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / Winged helix-like DNA-binding domain superfamily / WD40/YVTN repeat-like-containing domain superfamily

Component:

Polyubiquitin-C / Ubiquitin-conjugating enzyme E2 D2 / E3 ubiquitin-protein ligase RBX1 / DNA excision repair protein ERCC-8 / Cullin-4A / NEDD8 / DNA damage-binding protein 1

• Biological species: Homo sapiens (human)
• Method: single particle reconstruction / cryo EM / Resolution: 3.5 Å
• Authors: Kokic G / Cramer P

Funding support

Germany, European Union, 2 items

Organization	Grant number	Country
German Research Foundation (DFG)	EXC 2067/1-390729940	Germany
European Research Council (ERC)	Advanced Investigator Grant CHROMATRANS (grant agreement No. 882357)	European Union

• Citation: Journal: To Be Published; Title: C(N)RL4CSA-E2-Ub (state 2); Authors: Kokic G / Cramer P

History

Deposition	Sep 16, 2022	-
Header (metadata) release	Sep 27, 2023	-
Map release	Sep 27, 2023	-
Update	Sep 27, 2023	-
Current status	Sep 27, 2023	Processing site: PDBe / Status: Released