+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0144 | |||||||||
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Title | Human apo-ferritin reconstructed in RELION-3.0 | |||||||||
Map data | Human apo-ferritin reconstructed in RELION-3.0 | |||||||||
Sample |
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Function / homology | Function and homology information iron ion sequestering activity / ferritin complex / Scavenging by Class A Receptors / negative regulation of ferroptosis / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation ...iron ion sequestering activity / ferritin complex / Scavenging by Class A Receptors / negative regulation of ferroptosis / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation / autophagosome / 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 / immune response / iron ion binding / negative regulation of cell population proliferation / Neutrophil degranulation / extracellular exosome / extracellular region / identical protein binding / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 1.65 Å | |||||||||
Authors | Zivanov J / Nakane T / Hagen WJH / Scheres SHW | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: Elife / Year: 2018 Title: New tools for automated high-resolution cryo-EM structure determination in RELION-3. Authors: Jasenko Zivanov / Takanori Nakane / Björn O Forsberg / Dari Kimanius / Wim Jh Hagen / Erik Lindahl / Sjors Hw Scheres / Abstract: Here, we describe the third major release of RELION. CPU-based vector acceleration has been added in addition to GPU support, which provides flexibility in use of resources and avoids memory ...Here, we describe the third major release of RELION. CPU-based vector acceleration has been added in addition to GPU support, which provides flexibility in use of resources and avoids memory limitations. Reference-free autopicking with Laplacian-of-Gaussian filtering and execution of jobs from python allows non-interactive processing during acquisition, including 2D-classification, model generation and 3D-classification. Per-particle refinement of CTF parameters and correction of estimated beam tilt provides higher resolution reconstructions when particles are at different heights in the ice, and/or coma-free alignment has not been optimal. Ewald sphere curvature correction improves resolution for large particles. We illustrate these developments with publicly available data sets: together with a Bayesian approach to beam-induced motion correction it leads to resolution improvements of 0.2-0.7 Å compared to previous RELION versions. | |||||||||
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_0144.map.gz | 166.8 MB | EMDB map data format | |
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Header (meta data) | emd-0144-v30.xml emd-0144.xml | 15.4 KB 15.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_0144_fsc.xml | 12.6 KB | Display | FSC data file |
Images | emd_0144.png | 219.6 KB | ||
Masks | emd_0144_msk_1.map | 178 MB | Mask map | |
Others | emd_0144_half_map_1.map.gz emd_0144_half_map_2.map.gz | 135.7 MB 135.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0144 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0144 | HTTPS FTP |
-Validation report
Summary document | emd_0144_validation.pdf.gz | 326.1 KB | Display | EMDB validaton report |
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Full document | emd_0144_full_validation.pdf.gz | 325.2 KB | Display | |
Data in XML | emd_0144_validation.xml.gz | 18.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0144 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0144 | HTTPS FTP |
-Related structure data
Related structure data | 0152C 0153C 0263C C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10200 (Title: Human apo-ferritin reconstructed in RELION-3.0 / Data size: 191.5 Data #1: Unaligned multi-frame micrographs (in non-gain-corrected TIFF) of human apo-ferritin [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_0144.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Human apo-ferritin reconstructed in RELION-3.0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.814 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_0144_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Independently refined half-map 1
File | emd_0144_half_map_1.map | ||||||||||||
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Annotation | Independently refined half-map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Independently refined half-map 2
File | emd_0144_half_map_2.map | ||||||||||||
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Annotation | Independently refined half-map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : human apo-ferritin
Entire | Name: human apo-ferritin |
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Components |
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-Supramolecule #1: human apo-ferritin
Supramolecule | Name: human apo-ferritin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 440 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Alignment procedure | Coma free - Residual tilt: 0.05 mrad |
Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Details | Used beam shift to collect seven images within one 1.2um Quantifoil hole. Used active beamtilt compensation in TEM microscope software. |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 1255 / Average electron dose: 47.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated defocus max: 8.0 µm / Calibrated defocus min: 0.5 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |