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Open data
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Basic information
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Title | High resolution of apo-ferritin embedded in crystalline ice | |||||||||
![]() | EM map of Human apo-ferritin embedded in crystal datasets frozen at -183 degree collected via Titan Krios by K2 camera. | |||||||||
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![]() | complex / Transport Protein | |||||||||
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 / Resolution: 1.76 Å | |||||||||
![]() | Zhang X / Shi H / Wu C | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Addressing compressive deformation of proteins embedded in crystalline ice. Authors: Huigang Shi / Chunling Wu / Xinzheng Zhang / ![]() Abstract: For cryoelectron microscopy (cryo-EM), high cooling rates have been required for preparation of protein samples to vitrify the surrounding water and avoid formation of damaging crystalline ice. ...For cryoelectron microscopy (cryo-EM), high cooling rates have been required for preparation of protein samples to vitrify the surrounding water and avoid formation of damaging crystalline ice. Whether and how crystalline ice affects single-particle cryo-EM is still unclear. Here, single-particle cryo-EM was used to analyze three-dimensional structures of various proteins and viruses embedded in crystalline ice formed at various cooling rates. Low cooling rates led to shrinkage deformation and density distortions on samples having loose structures. Higher cooling rates reduced deformations. Deformation-free proteins in crystalline ice were obtained by modifying the freezing conditions, and reconstructions from these samples revealed a marked improvement over vitreous ice. This procedure also increased the efficiency of cryo-EM structure determinations and was essential for high-resolution reconstructions. | |||||||||
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Structure visualization
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Downloads & links
-EMDB archive
Map data | ![]() | 95.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 11.9 KB 11.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.6 KB | Display | ![]() |
Images | ![]() | 89.7 KB | ||
Filedesc metadata | ![]() | 3.8 KB | ||
Others | ![]() ![]() | 87.7 MB 87.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 17.7 KB | Display | |
Data in CIF | ![]() | 23.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8f49MC ![]() 8bqnC ![]() 8ew0C ![]() 8ew2C ![]() 8f7yC ![]() 8hhsC ![]() 8hi2C M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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 | EM map of Human apo-ferritin embedded in crystal datasets frozen at -183 degree collected via Titan Krios by K2 camera. | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.52 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half map of Human apo-ferritin embedded in crystal...
File | emd_32695_half_map_1.map | ||||||||||||
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Annotation | Half map of Human apo-ferritin embedded in crystal datasets frozen at -183 degree collected via Titan Krios by K2 camera. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map of Human apo-ferritin embedded in crystal...
File | emd_32695_half_map_2.map | ||||||||||||
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Annotation | Half map of Human apo-ferritin embedded in crystal datasets frozen at -183 degree collected via Titan Krios by K2 camera. | ||||||||||||
Projections & Slices |
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Density Histograms |
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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 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 440 KDa |
-Experimental details
-Structure determination
![]() | single particle reconstruction |
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Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Sugar embedding | Material: crystalline ice |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |