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Open data
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Basic information
Entry | Database: PDB / ID: 8wzk | |||||||||
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Title | Human erythrocyte catalase | |||||||||
![]() | Catalase | |||||||||
![]() | OXIDOREDUCTASE / Catalase / heme / NADP | |||||||||
Function / homology | ![]() response to phenylpropanoid / aminoacylase activity / catalase complex / hemoglobin metabolic process / response to inactivity / cellular detoxification of hydrogen peroxide / response to ozone / oxidoreductase activity, acting on peroxide as acceptor / response to L-ascorbic acid / catalase ...response to phenylpropanoid / aminoacylase activity / catalase complex / hemoglobin metabolic process / response to inactivity / cellular detoxification of hydrogen peroxide / response to ozone / oxidoreductase activity, acting on peroxide as acceptor / response to L-ascorbic acid / catalase / UV protection / response to fatty acid / response to light intensity / catalase activity / response to vitamin A / peroxisomal membrane / ureteric bud development / triglyceride metabolic process / Detoxification of Reactive Oxygen Species / antioxidant activity / peroxisomal matrix / positive regulation of cell division / response to vitamin E / response to hyperoxia / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / response to cadmium ion / cholesterol metabolic process / response to activity / response to reactive oxygen species / hydrogen peroxide catabolic process / Peroxisomal protein import / response to lead ion / response to insulin / response to hydrogen peroxide / aerobic respiration / cellular response to growth factor stimulus / osteoblast differentiation / response to estradiol / peroxisome / NADP binding / secretory granule lumen / response to ethanol / ficolin-1-rich granule lumen / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / response to hypoxia / response to xenobiotic stimulus / intracellular membrane-bounded organelle / focal adhesion / heme binding / Neutrophil degranulation / negative regulation of apoptotic process / enzyme binding / protein homodimerization activity / protein-containing complex / mitochondrion / extracellular exosome / extracellular region / identical protein binding / membrane / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.4 Å | |||||||||
![]() | Yadav, S. / Vinothkumar, K.R. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Factors affecting macromolecule orientations in thin films formed in cryo-EM. Authors: Swati Yadav / Kutti R Vinothkumar / ![]() Abstract: The formation of a vitrified thin film embedded with randomly oriented macromolecules is an essential prerequisite for cryogenic sample electron microscopy. Most commonly, this is achieved using the ...The formation of a vitrified thin film embedded with randomly oriented macromolecules is an essential prerequisite for cryogenic sample electron microscopy. Most commonly, this is achieved using the plunge-freeze method first described nearly 40 years ago. Although this is a robust method, the behaviour of different macromolecules shows great variation upon freezing and often needs to be optimized to obtain an isotropic, high-resolution reconstruction. For a macromolecule in such a film, the probability of encountering the air-water interface in the time between blotting and freezing and adopting preferred orientations is very high. 3D reconstruction using preferentially oriented particles often leads to anisotropic and uninterpretable maps. Currently, there are no general solutions to this prevalent issue, but several approaches largely focusing on sample preparation with the use of additives and novel grid modifications have been attempted. In this study, the effect of physical and chemical factors on the orientations of macromolecules was investigated through an analysis of selected well studied macromolecules, and important parameters that determine the behaviour of proteins on cryo-EM grids were revealed. These insights highlight the nature of the interactions that cause preferred orientations and can be utilized to systematically address orientation bias for any given macromolecule and to provide a framework to design small-molecule additives to enhance sample stability and behaviour. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 403.6 KB | Display | ![]() |
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PDB format | ![]() | 331.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 65.6 KB | Display | |
Data in CIF | ![]() | 95.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 37955MC ![]() 8wv4C ![]() 8wv5C ![]() 8wv6C ![]() 8wzhC ![]() 8wziC ![]() 8wzjC ![]() 8wzmC C: citing same article ( M: map data used to model this data |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
#1: Protein | Mass: 59836.996 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Chemical | ChemComp-HEM / #3: Chemical | ChemComp-NDP / Has ligand of interest | N | |
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-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 erythrocyte catalase / Type: COMPLEX / Entity ID: #1 / Source: NATURAL |
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Molecular weight | Value: 0.238 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() |
Buffer solution | pH: 8 |
Buffer component | Conc.: 50 mM / Name: Tris |
Specimen | Conc.: 0.625 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / 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 |
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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 / Nominal magnification: 75000 X / Calibrated magnification: 130841 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 60 sec. / Electron dose: 25 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) Details: Images were collected in movie mode at 40 frames per second. Total of 25 frames were saved for each movie. |
Image scans | Sampling size: 14 µm / Width: 4096 / Height: 4096 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: D2 (2x2 fold dihedral) | ||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 478656 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 104.5 / Protocol: OTHER / Space: RECIPROCAL | ||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 1DGF Accession code: 1DGF / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||||||||||||||||||
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