+Open data
-Basic information
Entry | Database: PDB / ID: 8alz | ||||||||||||||||||
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Title | Cryo-EM structure of ASCC3 in complex with ASC1 | ||||||||||||||||||
Components |
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Keywords | DNA BINDING PROTEIN / helicase / zinc finger / activator / DNA binding | ||||||||||||||||||
Function / homology | Function and homology information ALKBH3 mediated reversal of alkylation damage / activating signal cointegrator 1 complex / regulation of myoblast differentiation / DNA alkylation repair / ribosome disassembly / ribosome-associated ubiquitin-dependent protein catabolic process / DNA duplex unwinding / histone acetyltransferase binding / ubiquitin-like protein ligase binding / 3'-5' DNA helicase activity ...ALKBH3 mediated reversal of alkylation damage / activating signal cointegrator 1 complex / regulation of myoblast differentiation / DNA alkylation repair / ribosome disassembly / ribosome-associated ubiquitin-dependent protein catabolic process / DNA duplex unwinding / histone acetyltransferase binding / ubiquitin-like protein ligase binding / 3'-5' DNA helicase activity / estrogen receptor signaling pathway / rescue of stalled ribosome / nuclear estrogen receptor binding / nuclear receptor binding / neuromuscular junction / DNA helicase / protease binding / cell population proliferation / transcription coactivator activity / nuclear body / nuclear speck / centrosome / regulation of DNA-templated transcription / protein kinase binding / positive regulation of DNA-templated transcription / protein-containing complex / RNA binding / zinc ion binding / nucleoplasm / ATP binding / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||||||||||||||
Authors | Jia, J. / Hilal, T. / Loll, B. / Wahl, M.C. | ||||||||||||||||||
Funding support | Germany, 5items
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Citation | Journal: Nat Commun / Year: 2023 Title: Cryo-EM structure of ASCC3 in complex with ASC1 Authors: Jia, J. / Hilal, T. / Loll, B. / Wahl, M.C. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8alz.cif.gz | 384.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8alz.ent.gz | 299 KB | Display | PDB format |
PDBx/mmJSON format | 8alz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8alz_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8alz_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8alz_validation.xml.gz | 71.8 KB | Display | |
Data in CIF | 8alz_validation.cif.gz | 105.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/al/8alz ftp://data.pdbj.org/pub/pdb/validation_reports/al/8alz | HTTPS FTP |
-Related structure data
Related structure data | 15521MC 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: 66650.656 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TRIP4, RQT4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q15650 | ||
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#2: Protein | Mass: 206276.094 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ASCC3, HELIC1, RQT2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8N3C0, DNA helicase | ||
#3: Chemical | Has ligand of interest | N | |
-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: ASCC3-ASC1 / Type: COMPLEX Details: Protein complex was produced in baculovirus-insect system. Entity ID: #1-#2 / Source: RECOMBINANT | |||||||||||||||||||||||||
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Molecular weight | Value: 0.27 MDa / Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: Homo sapiens (human) | |||||||||||||||||||||||||
Source (recombinant) | Organism: Trichoplusia ni (cabbage looper) | |||||||||||||||||||||||||
Buffer solution | pH: 7.5 Details: Solutions were made fresh from concentrated to avoid microbial contamination. | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 4.15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse. | |||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283.15 K |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Alignment procedure: ZEMLIN TABLEAU |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 40.57 sec. / Electron dose: 42 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 6267 |
-Processing
Software | Name: PHENIX / Version: 1.20_4459: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 244064 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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