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Yorodumi- EMDB-60915: Cryo-EM structure of mouse heavy-chain apoferritin resolved at 1.... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-60915 | |||||||||
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Title | Cryo-EM structure of mouse heavy-chain apoferritin resolved at 1.51 Angstroms | |||||||||
Map data | ||||||||||
Sample |
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Keywords | cryo-EM / mouse / heavy-chain apoferritin / Mus musculus / OXIDOREDUCTASE | |||||||||
Function / homology | Function and homology information 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 | Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 1.51 Å | |||||||||
Authors | Wang CH / Wu KP / Chang YC | |||||||||
Funding support | Taiwan, 1 items
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Citation | Journal: To Be Published Title: Cryo-EM structure of mouse heavy-chain apoferritin resolved at 1.51 Angstroms Authors: Wang CH / Wu KP / Chang YC | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_60915.map.gz | 203.9 MB | EMDB map data format | |
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Header (meta data) | emd-60915-v30.xml emd-60915.xml | 14.3 KB 14.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_60915_fsc.xml | 12.5 KB | Display | FSC data file |
Images | emd_60915.png | 319.5 KB | ||
Filedesc metadata | emd-60915.cif.gz | 5.3 KB | ||
Others | emd_60915_half_map_1.map.gz emd_60915_half_map_2.map.gz | 200 MB 200 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-60915 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-60915 | HTTPS FTP |
-Related structure data
Related structure data | 9iuy M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_60915.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.648 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_60915_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_60915_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Homo 24-mer of mouse heavy-chain apoferritin (Octahedral symmetry)
Entire | Name: Homo 24-mer of mouse heavy-chain apoferritin (Octahedral symmetry) |
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Components |
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-Supramolecule #1: Homo 24-mer of mouse heavy-chain apoferritin (Octahedral symmetry)
Supramolecule | Name: Homo 24-mer of mouse heavy-chain apoferritin (Octahedral symmetry) type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Mus musculus (house mouse) |
-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: Mus musculus (house mouse) |
Molecular weight | Theoretical: 21.097631 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MTTASPSQVR QNYHQDAEAA INRQINLELY ASYVYLSMSC YFDRDDVALK NFAKYFLHQS HEEREHAEKL MKLQNQRGGR IFLQDIKKP DRDDWESGLN AMECALHLEK SVNQSLLELH KLATDKNDPH LCDFIETYYL SEQVKSIKEL GDHVTNLRKM G APEAGMAE YLFDKHTLGH GDES UniProtKB: Ferritin heavy chain |
-Macromolecule #2: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 32 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #3: POTASSIUM ION
Macromolecule | Name: POTASSIUM ION / type: ligand / ID: 3 / Number of copies: 24 / Formula: K |
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Molecular weight | Theoretical: 39.098 Da |
-Macromolecule #4: FE (III) ION
Macromolecule | Name: FE (III) ION / type: ligand / ID: 4 / Number of copies: 6 / Formula: FE |
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Molecular weight | Theoretical: 55.845 Da |
-Macromolecule #5: water
Macromolecule | Name: water / type: ligand / ID: 5 / Number of copies: 3288 / 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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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 / Details: 30 mM HEPES, 150 mM NaCl, 1mM DTT |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
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 FIELD / Cs: 2.7 mm / Nominal defocus max: 2.251 µm / Nominal defocus min: 0.582 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |