- EMDB-31766: CryoEM structure of DDB1-VprBP-Vpr-UNG2(94-313) complex -
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Basic information
Entry
Database: EMDB / ID: EMD-31766
Title
CryoEM structure of DDB1-VprBP-Vpr-UNG2(94-313) complex
Map data
Sample
Complex: DDB1-VprBP-Vpr-UNG2(94-313) complex
Protein or peptide: DDB1- and CUL4-associated factor 1
Protein or peptide: DNA damage-binding protein 1
Protein or peptide: Protein Vpr
Protein or peptide: Uracil-DNA glycosylase
Function / homology
Function and homology information
: / histone H2AT120 kinase activity / cell competition in a multicellular organism / symbiont-mediated arrest of host cell cycle during G2/M transition / base-excision repair, AP site formation via deaminated base removal / uracil-DNA glycosylase / depyrimidination / Displacement of DNA glycosylase by APEX1 / positive regulation by virus of viral protein levels in host cell / V(D)J recombination ...: / histone H2AT120 kinase activity / cell competition in a multicellular organism / symbiont-mediated arrest of host cell cycle during G2/M transition / base-excision repair, AP site formation via deaminated base removal / uracil-DNA glycosylase / depyrimidination / Displacement of DNA glycosylase by APEX1 / positive regulation by virus of viral protein levels in host cell / V(D)J recombination / epigenetic programming in the zygotic pronuclei / isotype switching / spindle assembly involved in female meiosis / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / uracil DNA N-glycosylase activity / biological process involved in interaction with symbiont / WD40-repeat domain binding / regulation of mitotic cell cycle phase transition / 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 / cullin family protein binding / ribosomal small subunit binding / ubiquitin-like ligase-substrate adaptor activity / viral release from host cell / ectopic germ cell programmed cell death / proteasomal protein catabolic process / positive regulation of viral genome replication / somatic hypermutation of immunoglobulin genes / monoatomic ion transport / positive regulation of gluconeogenesis / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / B cell differentiation / post-translational protein modification / Chromatin modifications during the maternal to zygotic transition (MZT) / virion component / nuclear estrogen receptor binding / nucleotide-excision repair / Recognition of DNA damage by PCNA-containing replication complex / DNA Damage Recognition in GG-NER / base-excision repair / protein homooligomerization / regulation of circadian rhythm / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / fibrillar center / Wnt signaling pathway / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / viral penetration into host nucleus / positive regulation of protein catabolic process / cellular response to UV / rhythmic process / Antigen processing: Ubiquitination & Proteasome degradation / protein-macromolecule adaptor activity / Neddylation / site of double-strand break / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / host extracellular space / chromosome, telomeric region / damaged DNA binding / non-specific serine/threonine protein kinase / protein ubiquitination / symbiont entry into host cell / cell cycle / phosphorylation / DNA repair / protein serine kinase activity / DNA-templated transcription / apoptotic process / DNA damage response / host cell nucleus / protein-containing complex binding / regulation of DNA-templated transcription / nucleolus / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / DNA binding / extracellular space / extracellular exosome / nucleoplasm / ATP binding / nucleus / cytoplasm Similarity search - Function
Retroviral VpR/VpX protein / VPR/VPX protein / VPRBP/DCAF1 family / Uracil-DNA glycosylase family 1 / Lissencephaly type-1-like homology motif / UreE urease accessory protein, C-terminal domain / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / Uracil-DNA glycosylase-like ...Retroviral VpR/VpX protein / VPR/VPX protein / VPRBP/DCAF1 family / Uracil-DNA glycosylase family 1 / Lissencephaly type-1-like homology motif / UreE urease accessory protein, C-terminal domain / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / Uracil-DNA glycosylase-like / Uracil DNA glycosylase superfamily / LIS1 homology (LisH) motif profile. / LIS1 homology motif / Uracil-DNA glycosylase-like domain superfamily / 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 / Armadillo-like helical / Armadillo-type fold / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily Similarity search - Domain/homology
Protein Vpr / Uracil-DNA glycosylase / DNA damage-binding protein 1 / DDB1- and CUL4-associated factor 1 Similarity search - Component
Biological species
Homo sapiens (human) / Human immunodeficiency virus 1
Method
single particle reconstruction / cryo EM / Resolution: 3.7 Å
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