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- EMDB-21024: Single-particle cryo-EM reconstruction of mouse heavy chain apofe... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-21024 | |||||||||
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Title | Single-particle cryo-EM reconstruction of mouse heavy chain apoferritin at 200 keV | |||||||||
![]() | Single-particle cryo-EM reconstruction of mouse heavy chain apoferritin using 200 keV | |||||||||
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![]() | homo-24-mer / storage / globular / METAL BINDING PROTEIN / OXIDOREDUCTASE | |||||||||
Function / homology | ![]() Iron uptake and transport / Golgi Associated Vesicle Biogenesis / iron ion sequestering activity / negative regulation of ferroptosis / autolysosome / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation / endocytic vesicle lumen ...Iron uptake and transport / Golgi Associated Vesicle Biogenesis / iron ion sequestering activity / negative regulation of ferroptosis / autolysosome / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation / endocytic vesicle lumen / Neutrophil degranulation / ferric iron binding / ferrous iron binding / iron ion transport / iron ion binding / immune response / negative regulation of cell population proliferation / mitochondrion / extracellular region / identical protein binding / membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 1.75 Å | |||||||||
![]() | Wu M / Lander GC | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Sub-2 Angstrom resolution structure determination using single-particle cryo-EM at 200 keV. Authors: Mengyu Wu / Gabriel C Lander / Mark A Herzik / ![]() Abstract: Although the advent of direct electron detectors (DEDs) and software developments have enabled the routine use of single-particle cryogenic electron microscopy (cryo-EM) for structure determination ...Although the advent of direct electron detectors (DEDs) and software developments have enabled the routine use of single-particle cryogenic electron microscopy (cryo-EM) for structure determination of well-behaved specimens to high-resolution, there nonetheless remains a discrepancy between the resolutions attained for biological specimens and the information limits of modern transmission electron microscopes (TEMs). Instruments operating at 300 kV equipped with DEDs are the current paradigm for high-resolution single-particle cryo-EM, while 200 kV TEMs remain comparatively underutilized for purposes beyond sample screening. Here, we expand upon our prior work and demonstrate that one such 200 kV microscope, the Talos Arctica, equipped with a K2 DED is capable of determining structures of macromolecules to as high as ∼1.7 Å resolution. At this resolution, ordered water molecules are readily assigned and holes in aromatic residues can be clearly distinguished in the reconstructions. This work emphasizes the utility of 200 kV electrons for high-resolution single-particle cryo-EM and applications such as structure-based drug design. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 201.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 20.7 KB 20.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 13.6 KB | Display | ![]() |
Images | ![]() | 243.2 KB | ||
Masks | ![]() | 216 MB | ![]() | |
Filedesc metadata | ![]() | 6.3 KB | ||
Others | ![]() ![]() ![]() | 165.9 MB 166.3 MB 166.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6v21MC ![]() 6v20C M: atomic model generated by this map C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data size: 549.5 Data #1: Mouse heavy-chain apoferritin movies obtained using a Talos Arctica (200 kV) equipped with a K2 [micrographs - multiframe]) |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Single-particle cryo-EM reconstruction of mouse heavy chain apoferritin using 200 keV | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.562 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Density Histograms |
-Additional map: Unsharpened map
File | emd_21024_additional.map | ||||||||||||
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Annotation | Unsharpened map | ||||||||||||
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Density Histograms |
-Half map: Even half map
File | emd_21024_half_map_1.map | ||||||||||||
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Annotation | Even half map | ||||||||||||
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Density Histograms |
-Half map: Odd half map
File | emd_21024_half_map_2.map | ||||||||||||
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Annotation | Odd half map | ||||||||||||
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Density Histograms |
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Sample components
-Entire : Heavy chain apoferritin from mouse
Entire | Name: Heavy chain apoferritin from mouse |
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Components |
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-Supramolecule #1: Heavy chain apoferritin from mouse
Supramolecule | Name: Heavy chain apoferritin from mouse / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 Details: Recombinantly expressed and purified from E. coli BL21(DE3)pLys cells |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 505 KDa |
-Macromolecule #1: Ferritin heavy chain
Macromolecule | Name: Ferritin heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO / EC number: ferroxidase |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 20.304818 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: SPSQVRQNYH QDAEAAINRQ INLELYASYV YLSMSCYFDR DDVALKNFAK YFLHQSHEER EHAEKLMKLQ NQRGGRIFLQ DIKKPDRDD WESGLNAMEC ALHLEKSVNQ SLLELHKLAT DKNDPHLCDF IETYYLSEQV KSIKELGDHV TNLRKMGAPE A GMAEYLFD KHTLGH UniProtKB: Ferritin heavy chain |
-Macromolecule #2: water
Macromolecule | Name: water / type: ligand / ID: 2 / Number of copies: 1783 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ![]() ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 4 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil, UltrAuFoil, R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 6 sec. / Pretreatment - Atmosphere: OTHER / Details: 15 Watts | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: HOMEMADE PLUNGER Details: 3 uL of sample/grid was manually blotted for 4 seconds prior to immediate plunge-freezing in liquid nitrogen-cooled ethane.. |
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Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 7420 pixel / Digitization - Dimensions - Height: 7676 pixel / Digitization - Frames/image: 1-90 / Number grids imaged: 1 / Number real images: 1759 / Average exposure time: 9.0 sec. / Average electron dose: 58.0 e/Å2 Details: Images were collected using stage position navigation to target exposure. |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 73000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |