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Open data
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Basic information
Entry | Database: PDB / ID: 7p8w | ||||||
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Title | Human erythrocyte catalase cryoEM | ||||||
![]() | Catalase | ||||||
![]() | OXIDOREDUCTASE / Human erythrocyte catalase cryoEM | ||||||
Function / homology | ![]() response to phenylpropanoid / aminoacylase activity / catalase complex / hemoglobin metabolic process / response to inactivity / cellular detoxification of hydrogen peroxide / response to L-ascorbic acid / response to ozone / oxidoreductase activity, acting on peroxide as acceptor / response to light intensity ...response to phenylpropanoid / aminoacylase activity / catalase complex / hemoglobin metabolic process / response to inactivity / cellular detoxification of hydrogen peroxide / response to L-ascorbic acid / response to ozone / oxidoreductase activity, acting on peroxide as acceptor / response to light intensity / catalase / UV protection / response to fatty acid / response to vitamin A / catalase activity / 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 / aerobic respiration / 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 / cellular response to growth factor stimulus / osteoblast differentiation / peroxisome / response to estradiol / 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: 2.2 Å | ||||||
![]() | Chen, S. / Li, J. / Vinothkumar, K.R. / Henderson, R. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Interaction of human erythrocyte catalase with air-water interface in cryoEM. Authors: Shaoxia Chen / Jade Li / Kutti R Vinothkumar / Richard Henderson / ![]() ![]() Abstract: One of the key goals in single-particle cryo-microscopy is to obtain a uniform distribution of particle orientations, so that the three-dimensional structure has isotropic resolution in Fourier space. ...One of the key goals in single-particle cryo-microscopy is to obtain a uniform distribution of particle orientations, so that the three-dimensional structure has isotropic resolution in Fourier space. A common problem arises from the interaction of protein molecules with the air-water interface that exists on both surfaces of the thin film of liquid that is formed prior to plunge-freezing into liquid ethane. Some proteins and other macromolecular complexes are disrupted by interaction with the air-water interface. Other proteins or macromolecules either become concentrated through their interaction with the interface or are excluded because they bind strongly to some other part of the grid or the filter paper used in blotting. In this paper, the interaction of human erythrocyte catalase with the air-water interface is investigated and minimized by the addition of certain detergents. Detergents can form an amphipathic monolayer at the air-water interface that creates a barrier and leaves the molecules free to adopt a variety of orientations, thus facilitating the 3D structure determination. These results suggest that further characterization and development of detergents for cryo-microscopy plunge-freezing would be useful. | ||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 433.2 KB | Display | ![]() |
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PDB format | ![]() | 352.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 59.3 KB | Display | |
Data in CIF | ![]() | 96.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 13256MC 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _ / Auth seq-ID: 4 - 505 / Label seq-ID: 4 - 505
NCS ensembles :
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Components
#1: Protein | Mass: 59836.996 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Chemical | ChemComp-NDP / #3: Chemical | ChemComp-HEM / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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 with cofactors Heme and NADPH Type: ORGANELLE OR CELLULAR COMPONENT / Details: Purified protein / Entity ID: #1 / Source: NATURAL | ||||||||||||||||||||
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Molecular weight | Value: 0.24 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: ![]() | ||||||||||||||||||||
Buffer solution | pH: 7.4 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 40 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: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K Details: Controlled environment plunge-freezer (Bellare et al, 1988; Technion University) |
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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 / 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 / Residual tilt: 0.25 mradians |
Image recording | Average exposure time: 59 sec. / Electron dose: 38 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 356 |
Image scans | Sampling size: 14 µm / Width: 4096 / Height: 4096 |
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Processing
Software | Name: REFMAC / Version: 5.8.0270 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: NONE | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 150000 / Details: Autopicked using RELION Laplacian operator | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: D2 (2x2 fold dihedral) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 119169 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 40 / Protocol: OTHER / Space: RECIPROCAL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | 3D fitting-ID: 1 / Source name: PDB / Type: experimental model
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Refinement | Resolution: 2.2→109.17 Å / Cor.coef. Fo:Fc: 0.854 / SU B: 5.34 / SU ML: 0.12 / ESU R: 0.224 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Solvent model: PARAMETERS FOR MASK CACLULATION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.369 Å2
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Refinement step | Cycle: 1 / Total: 17668 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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