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Yorodumi- EMDB-25619: CryoEM map of horse spleen apoferritin determined using MeasureIc... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-25619 | |||||||||
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Title | CryoEM map of horse spleen apoferritin determined using MeasureIce as a screening tool for ice thickness | |||||||||
Map data | ||||||||||
Sample |
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Keywords | iron storage / complex / METAL BINDING PROTEIN | |||||||||
Function / homology | Function and homology information intracellular ferritin complex / intracellular sequestering of iron ion / ferric iron binding / ferrous iron binding / iron ion transport / iron ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Equus caballus (horse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 1.88 Å | |||||||||
Authors | Hanssen E / Brown HG | |||||||||
Funding support | Australia, 1 items
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Citation | Journal: Commun Biol / Year: 2022 Title: MeasureIce: accessible on-the-fly measurement of ice thickness in cryo-electron microscopy Authors: Brown HG / Hanssen E | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_25619.map.gz | 303.5 MB | EMDB map data format | |
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Header (meta data) | emd-25619-v30.xml emd-25619.xml | 15.1 KB 15.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_25619_fsc.xml | 15.5 KB | Display | FSC data file |
Images | emd_25619.png | 271.9 KB | ||
Masks | emd_25619_msk_1.map | 325 MB | Mask map | |
Filedesc metadata | emd-25619.cif.gz | 4.7 KB | ||
Others | emd_25619_half_map_1.map.gz emd_25619_half_map_2.map.gz | 255.7 MB 255.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25619 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25619 | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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EM raw data | EMPIAR-11013 (Title: Cryo-EM images of equine apo-ferritin recorded as demonstration of MeasureIce software Data size: 127.4 Data #1: Unaligned multiframe micrographs of Equine Apoferritin [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_25619.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.637 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_25619_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_25619_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_25619_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Apoferritin from equine spleen
Entire | Name: Apoferritin from equine spleenFerritin |
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Components |
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-Supramolecule #1: Apoferritin from equine spleen
Supramolecule | Name: Apoferritin from equine spleen / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Equus caballus (horse) |
Molecular weight | Theoretical: 443 KDa |
-Macromolecule #1: Ferritin light chain
Macromolecule | Name: Ferritin light chain / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Equus caballus (horse) |
Sequence | String: SQIRQNYSTE VEAAVNRLVN LYLRASYTYL SLGFYFDRDD VALEGVCHFF RELAEEKREG AERLLKMQNQ RGGRALFQDL QKPSQDEWGT TLDAMKAAIV LEKSLNQALL DLHALGSAQA DPHLCDFLES HFLDEEVKLI KKMGDHLTNI QRLVGSQAGL GEYLFERLTL K UniProtKB: Ferritin light chain |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 / Component - Name: PBS |
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Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 120000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
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: 1 / Number real images: 619 / Average electron dose: 20.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |