[English] 日本語
Yorodumi- PDB-6z6u: 1.25 A structure of human apoferritin obtained from Titan Mono-BC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6z6u | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | 1.25 A structure of human apoferritin obtained from Titan Mono-BCOR microscope | |||||||||
Components | Ferritin heavy chain | |||||||||
Keywords | METAL BINDING PROTEIN / Apoferritin | |||||||||
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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.25 Å | |||||||||
Authors | Yip, K.M. / Fischer, N. / Paknia, E. / Chari, A. / Stark, H. | |||||||||
Funding support | Germany, 2items
| |||||||||
Citation | 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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6z6u.cif.gz | 2.5 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6z6u.ent.gz | 2.2 MB | Display | PDB format |
PDBx/mmJSON format | 6z6u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6z6u_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6z6u_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6z6u_validation.xml.gz | 116.5 KB | Display | |
Data in CIF | 6z6u_validation.cif.gz | 166.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z6/6z6u ftp://data.pdbj.org/pub/pdb/validation_reports/z6/6z6u | HTTPS FTP |
-Related structure data
Related structure data | 11103MC 6z9eC 6z9fC 7a6aC 7a6bC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | |
EM raw data | 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]) |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 21270.605 Da / Num. of mol.: 24 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FTH1, FTH, FTHL6, OK/SW-cl.84, PIG15 / Production host: Escherichia coli (E. coli) / References: UniProt: P02794, ferroxidase #2: Chemical | ChemComp-NA / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Apoferritin / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT |
---|---|
Molecular weight | Value: 500 kDa/nm / Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7 |
Specimen | Conc.: 3.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 120000 X / Nominal defocus max: 1000 nm / Nominal defocus min: 300 nm / Cs: 0.01 mm / Alignment procedure: ZEMLIN TABLEAU |
Image recording | Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) |
EM imaging optics | Chromatic aberration corrector: TFS Monochromator / Spherical aberration corrector: CEOS BCOR |
-Processing
EM software |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: NONE | |||||||||
Symmetry | Point symmetry: O (octahedral) | |||||||||
3D reconstruction | Resolution: 1.25 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1090676 / Algorithm: FOURIER SPACE / Symmetry type: POINT | |||||||||
Atomic model building | Space: RECIPROCAL |