+Open data
-Basic information
Entry | Database: PDB / ID: 8qh5 | |||||||||
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Title | CryoEM structure of UVSSA(VHS)-CSA-DDB1-DDA1 | |||||||||
Components |
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Keywords | LIGASE / Ubiquitin ligase / DNA repair | |||||||||
Function / homology | Function and homology information regulation of transcription-coupled nucleotide-excision repair / nucleotide-excision repair complex / single strand break repair / positive regulation by virus of viral protein levels in host cell / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / double-strand break repair via classical nonhomologous end joining / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / biological process involved in interaction with symbiont ...regulation of transcription-coupled nucleotide-excision repair / nucleotide-excision repair complex / single strand break repair / positive regulation by virus of viral protein levels in host cell / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / double-strand break repair via classical nonhomologous end joining / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / 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 / RNA polymerase II complex binding / viral release from host cell / cullin family protein binding / ectopic germ cell programmed cell death / response to X-ray / transcription-coupled nucleotide-excision repair / protein autoubiquitination / proteasomal protein catabolic process / positive regulation of viral genome replication / response to UV / positive regulation of gluconeogenesis / positive regulation of DNA repair / 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 / nuclear matrix / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / protein polyubiquitination / positive regulation of protein catabolic process / cellular response to UV / rhythmic process / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / site of double-strand break / Neddylation / chromosome / protein-macromolecule adaptor activity / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / response to oxidative stress / damaged DNA binding / chromosome, telomeric region / protein ubiquitination / DNA repair / DNA damage response / protein-containing complex binding / negative regulation of apoptotic process / nucleolus / apoptotic process / protein-containing complex / DNA binding / extracellular space / extracellular exosome / nucleoplasm / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Lee, S.-H. / Sixma, T.K. | |||||||||
Funding support | Netherlands, European Union, 2items
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Citation | Journal: To Be Published Title: CryoEM structure of UVSSA(VHS)-CSA-DDB1-DDA1 Authors: Lee, S.-H. / Sixma, T.K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8qh5.cif.gz | 513.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qh5.ent.gz | 407.5 KB | Display | PDB format |
PDBx/mmJSON format | 8qh5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qh5_validation.pdf.gz | 717.2 KB | Display | wwPDB validaton report |
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Full document | 8qh5_full_validation.pdf.gz | 739.7 KB | Display | |
Data in XML | 8qh5_validation.xml.gz | 49.6 KB | Display | |
Data in CIF | 8qh5_validation.cif.gz | 75.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qh/8qh5 ftp://data.pdbj.org/pub/pdb/validation_reports/qh/8qh5 | HTTPS FTP |
-Related structure data
Related structure data | 18398MC 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: 82923.164 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The construct contains an N-terminal His tag. / Source: (gene. exp.) Homo sapiens (human) / Gene: UVSSA, KIAA1530 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q2YD98 |
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#2: Protein | Mass: 45465.613 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The construct contains a Strep tag II at the C-terminus Source: (gene. exp.) Homo sapiens (human) / Gene: ERCC8, CKN1, CSA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q13216 |
#3: Protein | Mass: 129298.867 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The construct contains an N-terminal His tag. / Source: (gene. exp.) Homo sapiens (human) / Gene: DDB1, XAP1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q16531 |
#4: Protein | Mass: 16997.615 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The construct contains a TwinStrep tag and a Flag tag at the C-terminus. Source: (gene. exp.) Homo sapiens (human) / Gene: DDA1, C19orf58, PCIA1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9BW61 |
-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 UVSSA(VHS)-CSA-DDB1-DDA1 / Type: COMPLEX Details: Ternary complex of ubiquitinated UVSSA-USP7-CSA-DDB1-DDA1. USP7 is invisible in the cryoEM map. Entity ID: #2-#4, #1 / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Value: 0.21 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Homo sapiens (human) | ||||||||||||||||||||
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) | ||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.13 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was glutaraldehyde crosslinked | ||||||||||||||||||||
Specimen support | Details: The grid was coated with graphene oxide. / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS Details: Collected on Krios 1 at Netherlands Center for Electron Nanoscopy (NeCEN) |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1382 |
EM imaging optics | Energyfilter slit width: 20 eV |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 723908 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 294142 Details: Combined from focused maps reconstructed with various particle numbers. Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL Details: Additional densities are observed near several cysteine residues (A/Cys222, A/Cys260, A/Cys288, B/Cys363, B/Cys725, B/Cys1008). We expect these are oxidized products or crosslinking side products. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | 3D fitting-ID: 1
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