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Yorodumi- EMDB-3854: Cryo-EM structure of human apoferritin at 3.15 A resolution deter... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3854 | |||||||||
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Title | Cryo-EM structure of human apoferritin at 3.15 A resolution determined with the Volta phase plate | |||||||||
Map data | Cryo-EM structure of human apoferritin at 3.15 A determined with the Volta phase plate | |||||||||
Sample |
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Function / homology | Function and homology information iron ion sequestering activity / : / negative regulation of ferroptosis / autolysosome / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation ...iron ion sequestering activity / : / negative regulation of ferroptosis / autolysosome / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding / Iron uptake and transport / ferrous iron binding / tertiary granule lumen / iron ion transport / intracellular iron ion homeostasis / ficolin-1-rich granule lumen / iron ion binding / immune response / negative regulation of cell population proliferation / Neutrophil degranulation / extracellular exosome / extracellular region / identical protein binding / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.15 Å | |||||||||
Authors | Pechnikova EV | |||||||||
Citation | Journal: To Be Published Title: Cryo-EM structure of human apoferritin at 3.15 A resolution determined with the Volta phase plate Authors: Pechnikova EV | |||||||||
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_3854.map.gz | 10.6 MB | EMDB map data format | |
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Header (meta data) | emd-3854-v30.xml emd-3854.xml | 11 KB 11 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_3854_fsc.xml | 7 KB | Display | FSC data file |
Images | emd_3854.png | 88 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3854 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3854 | HTTPS FTP |
-Validation report
Summary document | emd_3854_validation.pdf.gz | 271.4 KB | Display | EMDB validaton report |
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Full document | emd_3854_full_validation.pdf.gz | 270.6 KB | Display | |
Data in XML | emd_3854_validation.xml.gz | 9.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3854 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3854 | HTTPS FTP |
-Related structure data
Related structure data | |
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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_3854.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of human apoferritin at 3.15 A determined with the Volta phase plate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.82 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : human h-ferritin
Entire | Name: human h-ferritin |
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Components |
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-Supramolecule #1: human h-ferritin
Supramolecule | Name: human h-ferritin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: The sample was prepared in National Laboratory of Biomacromolecules, IBP, China |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 509 KDa |
-Macromolecule #1: human h-ferritin
Macromolecule | Name: human h-ferritin / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: ferroxidase |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MTTASTSQVR QNYHQDSEAA INRQINLELY ASYVYLSMSY YFDRDDVALK NFAKYFLHQS HEEREHAEK LMKLQNQRGG RIFLQDIKKP DCDDWESGLN AMECALHLEK NVNQSLLELH K LATDKNDP HLCDFIETHY LNEQVKAIKE LGDHVTNLRK MGAPESGLAE YLFDKHTLGD SD NES |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 / Details: PBS |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Alignment procedure | Coma free - Residual tilt: 10.0 mrad |
Specialist optics | Phase plate: VOLTA PHASE PLATE |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average exposure time: 39.0 sec. / Average electron dose: 58.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: OTHER / Imaging mode: OTHER / Cs: 2.7 mm / Nominal magnification: 96000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |