- EMDB-23086: Structure of the human Fanconi anaemia Core-ID complex -
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Basic information
Entry
Database: EMDB / ID: EMD-23086
Title
Structure of the human Fanconi anaemia Core-ID complex
Map data
composite REFMAC5 map (masked) used in coordinate refinement
Sample
Complex: Human Fanconi Anaemia Core-ID complex
Protein or peptide: x 11 types
Ligand: x 1 types
Keywords
Complex / LIGASE
Function / homology
Function and homology information
regulation of germ cell proliferation / regulation of CD40 signaling pathway / Fanconi anaemia nuclear complex / regulation of regulatory T cell differentiation / male meiotic nuclear division / double-strand break repair involved in meiotic recombination / homologous chromosome pairing at meiosis / gamete generation / replication-born double-strand break repair via sister chromatid exchange / neuronal stem cell population maintenance ...regulation of germ cell proliferation / regulation of CD40 signaling pathway / Fanconi anaemia nuclear complex / regulation of regulatory T cell differentiation / male meiotic nuclear division / double-strand break repair involved in meiotic recombination / homologous chromosome pairing at meiosis / gamete generation / replication-born double-strand break repair via sister chromatid exchange / neuronal stem cell population maintenance / brain morphogenesis / DNA repair complex / mitotic intra-S DNA damage checkpoint signaling / myeloid cell homeostasis / condensed chromosome / female gonad development / protein monoubiquitination / germ cell development / spermatid development / positive regulation of double-strand break repair via homologous recombination / negative regulation of double-strand break repair via homologous recombination / interstrand cross-link repair / DNA polymerase binding / ovarian follicle development / removal of superoxide radicals / mitochondrion organization / nucleotide-excision repair / TP53 Regulates Transcription of DNA Repair Genes / response to gamma radiation / Fanconi Anemia Pathway / RING-type E3 ubiquitin transferase / response to radiation / PKR-mediated signaling / ubiquitin-protein transferase activity / chromosome / nuclear envelope / male gonad development / ubiquitin protein ligase activity / regulation of inflammatory response / regulation of cell population proliferation / cellular response to oxidative stress / protein-containing complex assembly / damaged DNA binding / nuclear body / DNA repair / intracellular membrane-bounded organelle / centrosome / DNA damage response / ubiquitin protein ligase binding / chromatin / nucleolus / mitochondrion / DNA binding / nucleoplasm / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function
Fanconi anaemia group C protein / Fanconi anemia-associated protein of 100kDa / Fanconi anemia group B protein / Fanconi anemia group G protein / Fanconi anaemia group C protein / Fanconi anemia-associated / Fanconi Anaemia group E protein, C-terminal / Fanconi anemia group F protein / FANCF, C-terminal domain superfamily / Fanconi anemia group E protein ...Fanconi anaemia group C protein / Fanconi anemia-associated protein of 100kDa / Fanconi anemia group B protein / Fanconi anemia group G protein / Fanconi anaemia group C protein / Fanconi anemia-associated / Fanconi Anaemia group E protein, C-terminal / Fanconi anemia group F protein / FANCF, C-terminal domain superfamily / Fanconi anemia group E protein / Fanconi anemia group F protein (FANCF) / Fanconi Anaemia group E protein FANCE / Fanconi anaemia group A protein / Fanconi anaemia group A protein, N-terminal domain / Fanconi anaemia group A protein / Fanconi anaemia group A protein N terminus / FANCL, UBC-like domain 2 / FANCL, UBC-like domain 3 / Fanconi anemia complex, subunit FancL, WD-repeat containing domain / E3 ubiquitin-protein ligase FANCL / FANCL C-terminal domain / FANCL, UBC-like domain 3 superfamily / FANCL UBC-like domain 1 / FANCL C-terminal domain / FANCL UBC-like domain 2 / FANCL UBC-like domain 3 / FANCL C-terminal domain / Fanconi anemia group I protein / FANCI solenoid 1 cap / FANCI solenoid 1 domain / FANCI helical domain 1 / FANCI helical domain 2 / FANCI solenoid 3 domain / FANCI solenoid 4 domain / FANCI solenoid 2 domain / FANCI solenoid 1 cap / FANCI solenoid 1 / FANCI solenoid 2 / FANCI solenoid 3 / FANCI solenoid 4 / FANCI helical domain 1 / FANCI helical domain 2 / Fanconi anaemia protein FANCD2 / Fanconi anaemia protein FancD2 nuclease / Ubiquitin-conjugating enzyme/RWD-like / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Zinc finger, RING/FYVE/PHD-type Similarity search - Domain/homology
Fanconi anemia, complementation group I / Fanconi anemia group G protein / Fanconi anemia group A protein / Fanconi anemia group C protein / Fanconi anemia core complex-associated protein 100 / Fanconi anemia group B protein / Fanconi anemia group D2 protein / Fanconi anemia group E protein / Fanconi anemia group F protein / E3 ubiquitin-protein ligase FANCL Similarity search - Component
Biological species
Homo sapiens (human)
Method
single particle reconstruction / cryo EM / Resolution: 4.3 Å
Journal: Nat Struct Mol Biol / Year: 2021 Title: Structure of the FA core ubiquitin ligase closing the ID clamp on DNA. Authors: Shengliu Wang / Renjing Wang / Christopher Peralta / Ayat Yaseen / Nikola P Pavletich / Abstract: The Fanconi anemia (FA) pathway is essential for the repair of DNA interstrand crosslinks. Central to the pathway is the FA core complex, a ubiquitin ligase of nine subunits that monoubiquitinates ...The Fanconi anemia (FA) pathway is essential for the repair of DNA interstrand crosslinks. Central to the pathway is the FA core complex, a ubiquitin ligase of nine subunits that monoubiquitinates the FANCI-FANCD2 (ID) DNA clamp. The 3.1 Å structure of the 1.1-MDa human FA core complex, described here, reveals an asymmetric assembly with two copies of all but the FANCC, FANCE and FANCF subunits. The asymmetry is crucial, as it prevents the binding of a second FANCC-FANCE-FANCF subcomplex that inhibits the recruitment of the UBE2T ubiquitin conjugating enzyme, and instead creates an ID binding site. A single active site then ubiquitinates FANCD2 and FANCI sequentially. We also present the 4.2-Å structures of the human core-UBE2T-ID-DNA complex in three conformations captured during monoubiquitination. They reveal the core-UBE2T complex remodeling the ID-DNA complex, closing the clamp on the DNA before ubiquitination. Monoubiquitination then prevents clamp opening after release from the core.
History
Deposition
Dec 10, 2020
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Header (metadata) release
Mar 10, 2021
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Map release
Mar 10, 2021
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Update
Mar 6, 2024
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Current status
Mar 6, 2024
Processing site: RCSB / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
focus3: reconstruction (masked) focused at FANCA' NTD, FANCG', FANCB-FAAP100 dimer of heterodimers, FANCEctd, FANCL' and the ID complex postprocessed with relion
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