+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4185 | |||||||||
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Title | Human GroEL obtained by grid-blotting from blue native PAGE | |||||||||
Map data | Grid blotted from blue native PAGE human GroEL | |||||||||
Sample |
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Function / homology | Function and homology information GroEL-GroES complex / chaperonin ATPase / virion assembly / chaperone cofactor-dependent protein refolding / isomerase activity / ATP-dependent protein folding chaperone / response to radiation / unfolded protein binding / protein folding / response to heat ...GroEL-GroES complex / chaperonin ATPase / virion assembly / chaperone cofactor-dependent protein refolding / isomerase activity / ATP-dependent protein folding chaperone / response to radiation / unfolded protein binding / protein folding / response to heat / protein refolding / magnesium ion binding / ATP hydrolysis activity / ATP binding / membrane / identical protein binding / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 25.0 Å | |||||||||
Authors | Kirykowicz AM / Woodward JD | |||||||||
Citation | Journal: To Be Published Title: Human GroEL obtained by grid-blotting from blue native PAGE Authors: Kirykowicz AM / Woodward JD | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4185.map.gz | 374.1 KB | EMDB map data format | |
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Header (meta data) | emd-4185-v30.xml emd-4185.xml | 8.9 KB 8.9 KB | Display Display | EMDB header |
Images | emd_4185.png | 27.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4185 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4185 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_4185.map.gz / Format: CCP4 / Size: 1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Grid blotted from blue native PAGE human GroEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.22 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : GroEL only
Entire | Name: GroEL only |
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Components |
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-Supramolecule #1: GroEL only
Supramolecule | Name: GroEL only / type: complex / ID: 1 / Parent: 0 / Details: Obtained from Sigma-Aldrich |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Molecular weight | Experimental: 840 KDa |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7 Details: Diluted in 50 mM Tris-HCl, 200 mM NaCl (pH 8.0). 1-5 ug of GroEL run on blue native page: Anode buffer: 25 mM Imidazole Cathode buffer A: 50 mM Tricine, 7.5 mM Imidazole, 0.02% Coomassie ...Details: Diluted in 50 mM Tris-HCl, 200 mM NaCl (pH 8.0). 1-5 ug of GroEL run on blue native page: Anode buffer: 25 mM Imidazole Cathode buffer A: 50 mM Tricine, 7.5 mM Imidazole, 0.02% Coomassie G250 (pH 7.0) Cathode buffer B: 50 mM Tricine, 7.5 mM Imidazole, 0.002% Coomassie G250 (pH 7.0) |
Staining | Type: NEGATIVE / Material: Uranyl Acetate Details: 1-5 ug of groEL was run on a blue native PAGE gel. Sample was transferred to grid by grid blotting procedure and washed/stained with 2% UA. |
Grid | Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: OTHER |
Details | Bought from Sigma-Aldrich (Germany) |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 1.2 mm / Nominal magnification: 50000 |
Image recording | Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average exposure time: 0.5 sec. / Average electron dose: 20.0 e/Å2 |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 463 / Details: Manual picking |
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Startup model | Type of model: OTHER Details: Starting model generated from EMAN Common Lines with C7 symmetry imposed |
Initial angle assignment | Type: COMMON LINE / Details: EMAN |
Final angle assignment | Type: PROJECTION MATCHING Details: EMAN procedure: 5 iteration of 10 degrees (19 classes generated), 5 iterations of 8 degrees (23 classes generated), 10 iterations of 5 degrees (61 classes generated), and 6 iterations of 3 ...Details: EMAN procedure: 5 iteration of 10 degrees (19 classes generated), 5 iterations of 8 degrees (23 classes generated), 10 iterations of 5 degrees (61 classes generated), and 6 iterations of 3 degrees (155 classes generated) |
Final reconstruction | Applied symmetry - Point group: D7 (2x7 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.5 CUT-OFF / Details: EMAN procedure / Number images used: 463 |