+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-19436 | |||||||||
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Title | Cryo-EM structure of mouse heavy-chain apoferritin | |||||||||
Map data | ||||||||||
Sample |
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Keywords | apoferritin / mouse / heavy-chain / high resolution / METAL BINDING PROTEIN | |||||||||
Function / homology | Function and homology information Iron uptake and transport / Golgi Associated Vesicle Biogenesis / negative regulation of ferroptosis / iron ion sequestering activity / 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 / negative regulation of ferroptosis / iron ion sequestering activity / 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 / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 1.09 Å | |||||||||
Authors | Nazarov S / Myasnikov A / Stahlberg H | |||||||||
Funding support | Switzerland, 1 items
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Citation | Journal: To Be Published Title: Cryo-EM structure of mouse heavy-chain apoferritin Authors: Nazarov S / Mohammed I / Kucukoglu B / Myasnikov A / Stahlberg H | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_19436.map.gz | 431.8 MB | EMDB map data format | |
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Header (meta data) | emd-19436-v30.xml emd-19436.xml | 17.1 KB 17.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_19436_fsc.xml | 26.3 KB | Display | FSC data file |
Images | emd_19436.png | 103.1 KB | ||
Masks | emd_19436_msk_1.map | 465.5 MB | Mask map | |
Filedesc metadata | emd-19436.cif.gz | 5.6 KB | ||
Others | emd_19436_additional_1.map.gz emd_19436_half_map_1.map.gz emd_19436_half_map_2.map.gz | 426.9 MB 431.5 MB 430.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-19436 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19436 | HTTPS FTP |
-Validation report
Summary document | emd_19436_validation.pdf.gz | 1.5 MB | Display | EMDB validaton report |
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Full document | emd_19436_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | emd_19436_validation.xml.gz | 30.1 KB | Display | |
Data in CIF | emd_19436_validation.cif.gz | 40.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19436 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19436 | HTTPS FTP |
-Related structure data
Related structure data | 8rqbMC M: atomic model generated by this map C: citing same article (ref.) |
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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_19436.map.gz / Format: CCP4 / Size: 465.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.30528 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_19436_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: #1
File | emd_19436_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_19436_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_19436_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Apoferritin from Mus musculus
Entire | Name: Apoferritin from Mus musculus |
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Components |
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-Supramolecule #1: Apoferritin from Mus musculus
Supramolecule | Name: Apoferritin from Mus musculus / 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, N-terminally processed
Macromolecule | Name: Ferritin heavy chain, N-terminally processed / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 20.079594 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: PSQVRQNYHQ DAEAAINRQI NLELYASYVY LSMSCYFDRD DVALKNFAKY FLHQSHEERE HAEKLMKLQN QRGGRIFLQD IKKPDRDDW ESGLNAMECA LHLEKSVNQS LLELHKLATD KNDPHLCDFI ETYYLSEQVK SIKELGDHVT NLRKMGAPEA G MAEYLFDK HTLG 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: 2622 / 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 | 8 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: LEICA EM GP |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.9 µm / Nominal defocus min: 0.3 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |