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- EMDB-21951: Cryo-EM Structure of Human Apoferritin Light Chain Vitrified Usin... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-21951 | ||||||||||||
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Title | Cryo-EM Structure of Human Apoferritin Light Chain Vitrified Using Back-it-up | ||||||||||||
![]() | Sharpened map | ||||||||||||
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![]() | Human / apoferritin / ferritin / light chain / back-it-up / through-grid wicking / METAL BINDING PROTEIN | ||||||||||||
Function / homology | ![]() : / autolysosome / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / intracellular sequestering of iron ion / ferric iron binding / Iron uptake and transport / ferrous iron binding / azurophil granule lumen / iron ion transport ...: / autolysosome / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / intracellular sequestering of iron ion / ferric iron binding / Iron uptake and transport / ferrous iron binding / azurophil granule lumen / iron ion transport / intracellular iron ion homeostasis / iron ion binding / Neutrophil degranulation / extracellular exosome / extracellular region / identical protein binding / membrane / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.0 Å | ||||||||||||
![]() | Tan YZ / Rubinstein JL | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Through-grid wicking enables high-speed cryoEM specimen preparation. Authors: Yong Zi Tan / John L Rubinstein / ![]() Abstract: Blotting times for conventional cryoEM specimen preparation complicate time-resolved studies and lead to some specimens adopting preferred orientations or denaturing at the air-water interface. Here, ...Blotting times for conventional cryoEM specimen preparation complicate time-resolved studies and lead to some specimens adopting preferred orientations or denaturing at the air-water interface. Here, it is shown that solution sprayed onto one side of a holey cryoEM grid can be wicked through the grid by a glass-fiber filter held against the opposite side, often called the `back', of the grid, producing a film suitable for vitrification. This process can be completed in tens of milliseconds. Ultrasonic specimen application and through-grid wicking were combined in a high-speed specimen-preparation device that was named `Back-it-up' or BIU. The high liquid-absorption capacity of the glass fiber compared with self-wicking grids makes the method relatively insensitive to the amount of sample applied. Consequently, through-grid wicking produces large areas of ice that are suitable for cryoEM for both soluble and detergent-solubilized protein complexes. The speed of the device increases the number of views for a specimen that suffers from preferred orientations. | ||||||||||||
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 | ![]() | 85.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 28 KB 28 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 11 KB | Display | ![]() |
Images | ![]() | 198.6 KB | ||
Masks | ![]() | 91.1 MB | ![]() | |
Filedesc metadata | ![]() | 6.3 KB | ||
Others | ![]() ![]() ![]() ![]() ![]() ![]() ![]() | 43.9 MB 7.9 MB 194.9 KB 20.5 MB 23.7 MB 84.1 MB 84.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6wx6MC ![]() 6wxbC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data size: 2.1 TB Data #1: Unaligned Falcon IV movie frames [micrographs - multiframe] Data #2: Aligned Dose-Weighted Micrographs [micrographs - single frame] Data #3: Final Particle Stack with Final Euler Angles and Shifts [picked particles - multiframe - processed]) |
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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 | Sharpened map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.816 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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-Additional map: Raw map
File | emd_21951_additional_1.map | ||||||||||||
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Annotation | Raw map | ||||||||||||
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-Additional map: Local resolution map
File | emd_21951_additional_2.map | ||||||||||||
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Annotation | Local resolution map | ||||||||||||
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Density Histograms |
-Additional map: 3DFSC - Thresholded and Binarized
File | emd_21951_additional_3.map | ||||||||||||
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Annotation | 3DFSC - Thresholded and Binarized | ||||||||||||
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-Additional map: 3DFSC - Thresholded
File | emd_21951_additional_4.map | ||||||||||||
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Annotation | 3DFSC - Thresholded | ||||||||||||
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-Additional map: 3DFSC - Raw
File | emd_21951_additional_5.map | ||||||||||||
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Annotation | 3DFSC - Raw | ||||||||||||
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Density Histograms |
-Half map: Half map 1
File | emd_21951_half_map_1.map | ||||||||||||
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Annotation | Half map 1 | ||||||||||||
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Density Histograms |
-Half map: Half map 2
File | emd_21951_half_map_2.map | ||||||||||||
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Annotation | Half map 2 | ||||||||||||
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Density Histograms |
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Sample components
-Entire : Human apoferritin light chain
Entire | Name: Human apoferritin light chain |
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Components |
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-Supramolecule #1: Human apoferritin light chain
Supramolecule | Name: Human apoferritin light chain / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 580 KDa |
-Macromolecule #1: Ferritin light chain
Macromolecule | Name: Ferritin light chain / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 24.275898 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: TGWSHPQFEK LKGGSSRGGG GGSGGSGGSG GSMSSQIRQN YSTDVEAAVN SLVNLYLQAS YTYLSLGFYF DRDDVALEGV SHFFRELAE EKREGYERLL KMQNQRGGRA LFQDIKKPAE DEWGKTPDAM KAAMALEKKL NQALLDLHAL GSARTDPHLC D FLETHFLD ...String: TGWSHPQFEK LKGGSSRGGG GGSGGSGGSG GSMSSQIRQN YSTDVEAAVN SLVNLYLQAS YTYLSLGFYF DRDDVALEGV SHFFRELAE EKREGYERLL KMQNQRGGRA LFQDIKKPAE DEWGKTPDAM KAAMALEKKL NQALLDLHAL GSARTDPHLC D FLETHFLD EEVKLIKKMG DHLTNLHRLG GPEAGLGEYL FERLTLRHDG GSGGSGGSGG SGGGASGGS UniProtKB: Ferritin light chain |
-Macromolecule #2: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 8 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Macromolecule #3: water
Macromolecule | Name: water / type: ligand / ID: 3 / Number of copies: 2420 / 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
Buffer | pH: 8 |
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Grid | Model: Homemade / Material: COPPER/RHODIUM / Support film - Material: GOLD / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: AIR Details: Both sides of the grid were glow discharged for 120 seconds. |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 50 % / Chamber temperature: 298 K / Instrument: HOMEMADE PLUNGER Details: Back-it-up (ultrasonic specimen application and through-grid wicking in a high-speed specimen preparation device) was used. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 2 / Number real images: 3168 / Average exposure time: 9.0 sec. / Average electron dose: 27.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |