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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-3853 | |||||||||
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Title | Cryo-EM structure of human apoferritin H | |||||||||
![]() | human apoferritin H | |||||||||
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Function / homology | ![]() iron ion sequestering activity / : / 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 ion sequestering activity / : / 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 | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.5 Å | |||||||||
![]() | Dudkina NV / Welsch S | |||||||||
![]() | ![]() Title: Falcon 3 Electron Counting detector enables high resolution cryo-EM structures Authors: Dudkina NV / Welsch S | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 9.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 13.9 KB 13.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 7.1 KB | Display | ![]() |
Images | ![]() | 64.3 KB | ||
Others | ![]() ![]() | 20.2 MB 20.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 298.1 KB | Display | ![]() |
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Full document | ![]() | 297.3 KB | Display | |
Data in XML | ![]() | 9.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | human apoferritin H | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.057 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: #1
File | emd_3853_additional.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: #1
File | emd_3853_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Human apoferritin H
Entire | Name: Human apoferritin H |
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Components |
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-Supramolecule #1: Human apoferritin H
Supramolecule | Name: Human apoferritin H / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() ![]() |
Molecular weight | Theoretical: 509 KDa |
-Macromolecule #1: Ferritin heavy chain
Macromolecule | Name: Ferritin heavy chain / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Sequence | String: MTTASTSQVR QNYHQDSEA A INRQINLE LY ASYVYLS MSY YFDRDD VALK NFAKY FLHQS HEER EHAEKL MKL QNQRGGR IF LQDIKKPD C DDWESGLNA MECALHLEKN VNQSLLELH K LATDKNDP HL CDFIETH YLN EQVKAI KELGDHVTNL RKMG ...String: MTTASTSQVR QNYHQDSEA A INRQINLE LY ASYVYLS MSY YFDRDD VALK NFAKY FLHQS HEER EHAEKL MKL QNQRGGR IF LQDIKKPD C DDWESGLNA MECALHLEKN VNQSLLELH K LATDKNDP HL CDFIETH YLN EQVKAI KELGDHVTNL RKMG APESG LAEYL FDKH TLGDSD NES |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 / Component - Formula: PBS |
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Grid | Model: Quantifoil / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV Details: Protein was applied to glow-discharged Quantifoil R2/2 grids. |
Details | The protein was provided by Institute of Biophysics of Chinese Academy of Sciences |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Alignment procedure | Coma free - Residual tilt: 10.0 mrad |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 14.0 µm / Number grids imaged: 1 / Number real images: 203 / Average exposure time: 55.0 sec. / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 75000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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