+Open data
-Basic information
Entry | Database: PDB / ID: 8t9a | ||||||
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Title | CryoEM structure of human DDB1-DCAF12 in complex with MAGEA3 | ||||||
Components |
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Keywords | LIGASE / DCAF12 / DNA damage-binding protein 1 / DDB1 / E3 ligase | ||||||
Function / homology | Function and homology information caspase binding / positive regulation by virus of viral protein levels in host cell / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / negative regulation of protein processing / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition ...caspase binding / positive regulation by virus of viral protein levels in host cell / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / negative regulation of protein processing / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4A-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / Cul4B-RING E3 ubiquitin ligase complex / negative regulation of reproductive process / negative regulation of developmental process / viral release from host cell / cullin family protein binding / ectopic germ cell programmed cell death / ubiquitin-like ligase-substrate adaptor activity / proteasomal protein catabolic process / positive regulation of viral genome replication / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / positive regulation of gluconeogenesis / negative regulation of autophagy / : / T cell activation / regulation of autophagy / nucleotide-excision repair / Recognition of DNA damage by PCNA-containing replication complex / DNA Damage Recognition in GG-NER / regulation of circadian rhythm / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Dual Incision in GG-NER / Wnt signaling pathway / histone deacetylase binding / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / positive regulation of protein catabolic process / cellular response to UV / rhythmic process / site of double-strand break / Neddylation / protein-macromolecule adaptor activity / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / damaged DNA binding / chromosome, telomeric region / protein ubiquitination / DNA repair / centrosome / DNA damage response / protein-containing complex binding / negative regulation of apoptotic process / nucleolus / apoptotic process / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / protein-containing complex / DNA binding / extracellular space / extracellular exosome / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.17 Å | ||||||
Authors | Duda, D. / Righetto, G. / Li, Y. / Loppnau, P. / Seitova, A. / Santhakumar, V. / Halabelian, L. / Yin, Y. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: CryoEM structure of human DDB1-DCAF12 in complex with MAGEA3 Authors: Duda, D. / Righetto, G. / Li, Y. / Loppnau, P. / Seitova, A. / Santhakumar, V. / Halabelian, L. / Yin, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8t9a.cif.gz | 279 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8t9a.ent.gz | 217.3 KB | Display | PDB format |
PDBx/mmJSON format | 8t9a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8t9a_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8t9a_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8t9a_validation.xml.gz | 52.4 KB | Display | |
Data in CIF | 8t9a_validation.cif.gz | 77.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t9/8t9a ftp://data.pdbj.org/pub/pdb/validation_reports/t9/8t9a | HTTPS FTP |
-Related structure data
Related structure data | 41105MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 127097.469 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DDB1, XAP1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q16531 |
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#2: Protein | Mass: 52760.512 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DCAF12, KIAA1892, TCC52, WDR40A / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q5T6F0 |
#3: Protein | Mass: 24032.760 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAGEA3, MAGE3 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P43357 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Ternary complex of DCAF12-DDB1-MAGEA3 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Buffer solution | pH: 8 |
Specimen | Conc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 4 K |
-Electron microscopy imaging
Microscopy | Model: TFS GLACIOS |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: DIFFRACTION / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 1 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 476215 / Symmetry type: POINT | ||||||||||||||||||||||||
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