- EMDB-11103: 1.25 A structure of human apoferritin obtained from Titan Mono-BC... -
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Basic information
Entry
Database: EMDB / ID: EMD-11103
Title
1.25 A structure of human apoferritin obtained from Titan Mono-BCOR microscope
Map data
Sample
Organelle or cellular component: Apoferritin
Protein or peptide: Ferritin heavy chain
Ligand: SODIUM ION
Ligand: MAGNESIUM ION
Ligand: water
Function / homology
Function and homology information
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
Journal: Nature / Year: 2020 Title: Atomic-resolution protein structure determination by cryo-EM. Authors: Ka Man Yip / Niels Fischer / Elham Paknia / Ashwin Chari / Holger Stark / Abstract: Single-particle electron cryo-microscopy (cryo-EM) is a powerful method for solving the three-dimensional structures of biological macromolecules. The technological development of transmission ...Single-particle electron cryo-microscopy (cryo-EM) is a powerful method for solving the three-dimensional structures of biological macromolecules. The technological development of transmission electron microscopes, detectors and automated procedures in combination with user-friendly image processing software and ever-increasing computational power have made cryo-EM a successful and expanding technology over the past decade. At resolutions better than 4 Å, atomic model building starts to become possible, but the direct visualization of true atomic positions in protein structure determination requires much higher (better than 1.5 Å) resolution, which so far has not been attained by cryo-EM. The direct visualization of atom positions is essential for understanding the mechanisms of protein-catalysed chemical reactions, and for studying how drugs bind to and interfere with the function of proteins. Here we report a 1.25 Å-resolution structure of apoferritin obtained by cryo-EM with a newly developed electron microscope that provides, to our knowledge, unprecedented structural detail. Our apoferritin structure has almost twice the 3D information content of the current world record reconstruction (at 1.54 Å resolution). We can visualize individual atoms in a protein, see density for hydrogen atoms and image single-atom chemical modifications. Beyond the nominal improvement in resolution, we also achieve a substantial improvement in the quality of the cryo-EM density map, which is highly relevant for using cryo-EM in structure-based drug design.
History
Deposition
May 29, 2020
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Header (metadata) release
Jun 24, 2020
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Map release
Jun 24, 2020
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Update
Feb 10, 2021
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Current status
Feb 10, 2021
Processing site: PDBe / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
EMPIAR-10591 (Title: Atomic resolution structure of apoferritin from Titan Mono/BCorr microscope Data size: 41.7 TB Data #1: Single particle cryo-EM dataset of apoferritin from Titan Mono-BCorr microscope at 1.25 angstrom resolution [micrographs - multiframe])
Applied symmetry - Point group: O (octahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 1.25 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1090676
Initial angle assignment
Type: NOT APPLICABLE
Final angle assignment
Type: NOT APPLICABLE
FSC plot (resolution estimation)
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Atomic model buiding 1
Refinement
Space: RECIPROCAL
Output model
PDB-6z6u: 1.25 A structure of human apoferritin obtained from Titan Mono-BCOR microscope
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