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Yorodumi- EMDB-23090: Structure of the human fanconi anaemia Core-UBE2T-ID-DNA complex ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23090 | |||||||||
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Title | Structure of the human fanconi anaemia Core-UBE2T-ID-DNA complex in closed state | |||||||||
Map data | composite REFMAC5 map (masked) used in coordinate refinement | |||||||||
Sample |
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Function / homology | Function and homology information regulation of germ cell proliferation / regulation of CD40 signaling pathway / Fanconi anaemia nuclear complex / protein K29-linked ubiquitination / protein K27-linked ubiquitination / regulation of regulatory T cell differentiation / double-strand break repair involved in meiotic recombination / male meiotic nuclear division / homologous chromosome pairing at meiosis / gamete generation ...regulation of germ cell proliferation / regulation of CD40 signaling pathway / Fanconi anaemia nuclear complex / protein K29-linked ubiquitination / protein K27-linked ubiquitination / regulation of regulatory T cell differentiation / double-strand break repair involved in meiotic recombination / male meiotic nuclear division / homologous chromosome pairing at meiosis / gamete generation / replication-born double-strand break repair via sister chromatid exchange / neuronal stem cell population maintenance / protein K6-linked ubiquitination / protein K11-linked ubiquitination / brain morphogenesis / DNA repair complex / mitotic intra-S DNA damage checkpoint signaling / myeloid cell homeostasis / E2 ubiquitin-conjugating enzyme / female gonad development / protein monoubiquitination / germ cell development / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / positive regulation of double-strand break repair via homologous recombination / spermatid development / protein autoubiquitination / protein K48-linked ubiquitination / negative regulation of double-strand break repair via homologous recombination / interstrand cross-link repair / DNA polymerase binding / ovarian follicle development / condensed chromosome / removal of superoxide radicals / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / mitochondrion organization / nucleotide-excision repair / Fanconi Anemia Pathway / response to gamma radiation / TP53 Regulates Transcription of DNA Repair Genes / RING-type E3 ubiquitin transferase / response to radiation / PKR-mediated signaling / protein polyubiquitination / ubiquitin-protein transferase activity / male gonad development / ubiquitin protein ligase activity / nuclear envelope / chromosome / regulation of cell population proliferation / cellular response to oxidative stress / regulation of inflammatory response / protein-containing complex assembly / damaged DNA binding / nuclear body / intracellular membrane-bounded organelle / DNA repair / centrosome / ubiquitin protein ligase binding / DNA damage response / chromatin binding / chromatin / nucleolus / mitochondrion / DNA binding / nucleoplasm / ATP binding / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Human (human) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||
Authors | Wang SL / Pavletich NP | |||||||||
Funding support | United States, 1 items
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Citation | 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_23090.map.gz | 62.8 MB | EMDB map data format | |
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Header (meta data) | emd-23090-v30.xml emd-23090.xml | 44.4 KB 44.4 KB | Display Display | EMDB header |
Images | emd_23090.png | 62.5 KB | ||
Others | emd_23090_additional_1.map.gz emd_23090_additional_2.map.gz emd_23090_additional_3.map.gz emd_23090_additional_4.map.gz emd_23090_additional_5.map.gz emd_23090_additional_6.map.gz | 16.5 MB 26.5 MB 18.1 MB 15.2 MB 16.2 MB 13.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23090 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23090 | HTTPS FTP |
-Validation report
Summary document | emd_23090_validation.pdf.gz | 309.8 KB | Display | EMDB validaton report |
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Full document | emd_23090_full_validation.pdf.gz | 309.4 KB | Display | |
Data in XML | emd_23090_validation.xml.gz | 7.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23090 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23090 | HTTPS FTP |
-Related structure data
Related structure data | 7kzvMC 7kzpC 7kzqC 7kzrC 7kzsC 7kztC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_23090.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | composite REFMAC5 map (masked) used in coordinate refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.056 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: focus1: reconstruction (masked) focused at FANCC-Entd-F-L-G and FANCB-FAAP100...
File | emd_23090_additional_1.map | ||||||||||||
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Annotation | focus1: reconstruction (masked) focused at FANCC-Entd-F-L-G and FANCB-FAAP100 WD40 domains postprocessed with relion | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: consensus reconstruction postprocessed with relion
File | emd_23090_additional_2.map | ||||||||||||
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Annotation | consensus reconstruction postprocessed with relion | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: focus2: reconstruction (masked) focused at FANCA' NTD, FANCG'-Ectd-L',...
File | emd_23090_additional_3.map | ||||||||||||
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Annotation | focus2: reconstruction (masked) focused at FANCA' NTD, FANCG'-Ectd-L', FANCB-FAAP100 dimer of heterodimers, the ID-DNA complex and UBE2T postprocessed with relion | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: focus3: reconstruction (masked) focused at FANCA-A' dimer and...
File | emd_23090_additional_4.map | ||||||||||||
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Annotation | focus3: reconstruction (masked) focused at FANCA-A' dimer and FANCG' postprocessed with relion | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: focus4: reconstruction (masked) focused at FANCEctd-FANCL', the ID-DNA...
File | emd_23090_additional_5.map | ||||||||||||
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Annotation | focus4: reconstruction (masked) focused at FANCEctd-FANCL', the ID-DNA complex and UBE2T postprocessed with relion | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: focus4 Ubiquitin plus: reconstruction (masked) focused at FANCEctd-FANCL', the ID-DNA...
File | emd_23090_additional_6.map | ||||||||||||
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Annotation | focus4_Ubiquitin_plus: reconstruction (masked) focused at FANCEctd-FANCL', the ID-DNA complex and UBE2T-Ubiquitin postprocessed with relion | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Human Fanconi Anaemia Core-UBE2T-ID-DNA complex
+Supramolecule #1: Human Fanconi Anaemia Core-UBE2T-ID-DNA complex
+Macromolecule #1: Fanconi anemia group A protein
+Macromolecule #2: Fanconi anemia group B protein
+Macromolecule #3: Fanconi anemia group C protein
+Macromolecule #4: Fanconi anemia group E protein
+Macromolecule #5: Fanconi anemia group F protein
+Macromolecule #6: Fanconi anemia group G protein
+Macromolecule #7: E3 ubiquitin-protein ligase FANCL
+Macromolecule #8: Fanconi anemia core complex-associated protein 100
+Macromolecule #9: Fanconi anemia core complex-associated protein 20
+Macromolecule #10: Ubiquitin-conjugating enzyme E2 T
+Macromolecule #11: Fanconi anemia, complementation group I
+Macromolecule #12: Fanconi anemia group D2 protein
+Macromolecule #13: DNA (29-MER)
+Macromolecule #14: DNA (29-MER)
+Macromolecule #15: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL | |||||||||||||||
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Buffer | pH: 8 Component:
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 36.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 74481 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |