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Open data
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Basic information
Entry | Database: PDB / ID: 7kzq | ||||||
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Title | Structure of the human Fanconi anaemia Core-ID complex | ||||||
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![]() | LIGASE / Complex | ||||||
Function / homology | ![]() 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 / 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 / condensed chromosome / 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 / 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 / nucleolus / mitochondrion / DNA binding / nucleoplasm / nucleus / metal ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å | ||||||
![]() | Wang, S.L. / Pavletich, N.P. | ||||||
Funding support | ![]()
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![]() | ![]() 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
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 8.2 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 23086MC ![]() 7kzpC ![]() 7kzrC ![]() 7kzsC ![]() 7kztC ![]() 7kzvC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Fanconi anemia group ... , 7 types, 10 molecules ASBOCEFGHV
#1: Protein | Mass: 165513.016 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Protein | Mass: 100640.172 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #3: Protein | | Mass: 66290.359 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #4: Protein | | Mass: 61026.086 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #5: Protein | | Mass: 45108.297 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #6: Protein | Mass: 70873.727 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #11: Protein | | Mass: 164325.516 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Protein , 2 types, 3 molecules LMU
#7: Protein | Mass: 45203.953 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: Q9NW38, RING-type E3 ubiquitin transferase #10: Protein | | Mass: 149512.078 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Fanconi anemia core complex-associated protein ... , 2 types, 3 molecules PQW
#8: Protein | Mass: 96513.898 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #9: Protein/peptide | | Mass: 4041.667 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Non-polymers , 1 types, 5 molecules ![](data/chem/img/ZN.gif)
#12: Chemical | ChemComp-ZN / |
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-Details
Has ligand of interest | N |
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Sequence details | The complete sequence of FAAP20 is MEAARRPRLGLSRRRPPPAGGPSGGRPWFLLGGDERERLWAELLRTVSPELILDHEVPSL ...The complete sequence of FAAP20 is MEAARRPRLG |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Human Fanconi Anaemia Core-ID complex / Type: COMPLEX / Entity ID: #1-#11 / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Value: 1.1 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: ![]() | ||||||||||||||||||||
Source (recombinant) | Organism: ![]() | ||||||||||||||||||||
Buffer solution | pH: 8 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 65 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
Software | Name: REFMAC / Version: 5.8.0267 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 76111 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Resolution: 4.3→4.3 Å / Cor.coef. Fo:Fc: 0.845 / SU B: 97.213 / SU ML: 0.541 / ESU R: 0.753 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 238.543 Å2
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Refinement step | Cycle: 1 / Total: 85546 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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