+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32703 | |||||||||
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Title | apo-ferritin embedded in crystalline ice frozen at -183 degree | |||||||||
Map data | Apo-ferritin map from crystal-embedded datasets frozen at -183 degree collected via FEI Arctica by K2 camera | |||||||||
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 / Resolution: 2.4 Å | |||||||||
Authors | Zhang X / Shi H / Wu C | |||||||||
Funding support | China, 1 items
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Citation | Journal: Structure / Year: 2023 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. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_32703.map.gz | 95.8 MB | EMDB map data format | |
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Header (meta data) | emd-32703-v30.xml emd-32703.xml | 23 KB 23 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_32703_fsc.xml | 13.5 KB | Display | FSC data file |
Images | emd_32703.png | 138.3 KB | ||
Masks | emd_32703_msk_1.map | 244.1 MB | Mask map | |
Others | emd_32703_additional_1.map.gz emd_32703_additional_2.map.gz emd_32703_additional_3.map.gz emd_32703_additional_4.map.gz emd_32703_additional_5.map.gz emd_32703_half_map_1.map.gz emd_32703_half_map_2.map.gz | 201.5 MB 59.9 MB 59.8 MB 59.8 MB 59.7 MB 188.2 MB 188.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32703 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32703 | HTTPS FTP |
-Related structure data
Related structure data | 8f4lM 8hhsMC 8bqnC 8ew0C 8ew2C 8f49C 8f7yC 8hi2C 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_32703.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Apo-ferritin map from crystal-embedded datasets frozen at -183 degree collected via FEI Arctica by K2 camera | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.5 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_32703_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Apo-ferritin map from standard freezing datasets collected via...
File | emd_32703_additional_1.map | ||||||||||||
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Annotation | Apo-ferritin map from standard freezing datasets collected via FEI Arctica by K2 camera | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Apo-ferritin map from crystal-embedded datasets frozen at -140...
File | emd_32703_additional_2.map | ||||||||||||
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Annotation | Apo-ferritin map from crystal-embedded datasets frozen at -140 degree collected via Titan Krios by K2 camera | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Apo-ferritin map from standard freezing datasets collected via...
File | emd_32703_additional_3.map | ||||||||||||
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Annotation | Apo-ferritin map from standard freezing datasets collected via Titan Krios by K2 camera | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Apo-ferritin map from crystal-embedded datasets frozen at -60...
File | emd_32703_additional_4.map | ||||||||||||
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Annotation | Apo-ferritin map from crystal-embedded datasets frozen at -60 degree collected via Titan Krios by K2 camera | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Apo-ferritin map from crystal-embedded datasets frozen at -100...
File | emd_32703_additional_5.map | ||||||||||||
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Annotation | Apo-ferritin map from crystal-embedded datasets frozen at -100 degree collected via Titan Krios by K2 camera | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Apo-ferritin map from crystal-embedded datasets frozen at -183...
File | emd_32703_half_map_1.map | ||||||||||||
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Annotation | Apo-ferritin map from crystal-embedded datasets frozen at -183 degree collected via FEI Arctica by K2 camera. The half map of apo-ferritin was flipped and centered. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Apo-ferritin map from crystal-embedded datasets frozen at -183...
File | emd_32703_half_map_2.map | ||||||||||||
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Annotation | Apo-ferritin map from crystal-embedded datasets frozen at -183 degree collected via FEI Arctica by K2 camera. The half map of apo-ferritin was flipped and centered. | ||||||||||||
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 / Chimera: Yes / Parent: 0 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 440 KDa |
-Experimental details
-Structure determination
Processing | single particle reconstruction |
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Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Sugar embedding | Material: crystalline ice |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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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: 200 kV / Electron source: FIELD EMISSION GUN |
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: Talos Arctica / Image courtesy: FEI Company |