+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10101 | |||||||||
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Title | Apoferritin from mouse at 1.84 angstrom resolution | |||||||||
Map data | ||||||||||
Sample |
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Keywords | iron ion binding / ferroxidase / iron storage / cytoplasm / METAL BINDING PROTEIN | |||||||||
Function / homology | Function and homology information Iron uptake and transport / Golgi Associated Vesicle Biogenesis / iron ion sequestering activity / negative regulation of ferroptosis / ferroxidase / autolysosome / 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 / ferroxidase / autolysosome / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation / endocytic vesicle lumen / autophagosome / Neutrophil degranulation / ferric iron binding / ferrous iron binding / iron ion transport / immune response / iron ion binding / 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: 1.84 Å | |||||||||
Authors | Mills DJ / Pfeil-Gardiner O / Vonck J | |||||||||
Citation | Journal: To Be Published Title: To be published later Authors: Vonck J / Mills DJ / Pfeil-Gardiner O | |||||||||
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_10101.map.gz | 96.6 MB | EMDB map data format | |
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Header (meta data) | emd-10101-v30.xml emd-10101.xml | 16.6 KB 16.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10101_fsc.xml | 10.6 KB | Display | FSC data file |
Images | emd_10101.png | 301.3 KB | ||
Filedesc metadata | emd-10101.cif.gz | 5.7 KB | ||
Others | emd_10101_half_map_1.map.gz emd_10101_half_map_2.map.gz | 75.7 MB 75.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10101 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10101 | HTTPS FTP |
-Validation report
Summary document | emd_10101_validation.pdf.gz | 927.3 KB | Display | EMDB validaton report |
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Full document | emd_10101_full_validation.pdf.gz | 926.9 KB | Display | |
Data in XML | emd_10101_validation.xml.gz | 18.2 KB | Display | |
Data in CIF | emd_10101_validation.cif.gz | 23.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10101 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10101 | HTTPS FTP |
-Related structure data
Related structure data | 6s61MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_10101.map.gz / Format: CCP4 / Size: 103 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: 0.656 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: mouse apoferritin, half map 1
File | emd_10101_half_map_1.map | ||||||||||||
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Annotation | mouse apoferritin, half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: mouse apoferritin, half map 2
File | emd_10101_half_map_2.map | ||||||||||||
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Annotation | mouse apoferritin, half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Octahedral complex of 24 apoferritin chains
Entire | Name: Octahedral complex of 24 apoferritin chains |
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Components |
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-Supramolecule #1: Octahedral complex of 24 apoferritin chains
Supramolecule | Name: Octahedral complex of 24 apoferritin chains / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 500 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: 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: FE (III) ION
Macromolecule | Name: FE (III) ION / type: ligand / ID: 2 / Number of copies: 6 / Formula: FE |
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Molecular weight | Theoretical: 55.845 Da |
-Macromolecule #3: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 3 / Number of copies: 24 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Macromolecule #4: water
Macromolecule | Name: water / type: ligand / ID: 4 / Number of copies: 3854 / 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
Concentration | 1.5 mg/mL | |||||||||
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Buffer | pH: 7.5 / Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 1788 / Average exposure time: 30.0 sec. / Average electron dose: 30.0 e/Å2 Details: Some images were discarding after motion correction (MotionCor2) and ctf estimation (CTFfind4), leaving 1745 for processing. |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated defocus max: 2.0 µm / Calibrated defocus min: 0.2 µm / Calibrated magnification: 182927 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / 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 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |