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Yorodumi- PDB-7vd8: 1.96 A structure of human apoferritin obtained from Talos Arctica... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7vd8 | ||||||||||||||||||
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Title | 1.96 A structure of human apoferritin obtained from Talos Arctica microscope | ||||||||||||||||||
Components | Ferritin heavy chain | ||||||||||||||||||
Keywords | STRUCTURAL 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: 1.96 Å | ||||||||||||||||||
Authors | Fan, H.C. / Zhang, Y. / Sun, F. | ||||||||||||||||||
Funding support | China, 5items
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Citation | Journal: Nat Commun / Year: 2021 Title: A cryo-electron microscopy support film formed by 2D crystals of hydrophobin HFBI. Authors: Hongcheng Fan / Bo Wang / Yan Zhang / Yun Zhu / Bo Song / Haijin Xu / Yujia Zhai / Mingqiang Qiao / Fei Sun / Abstract: Cryo-electron microscopy (cryo-EM) has become a powerful tool to resolve high-resolution structures of biomacromolecules in solution. However, air-water interface induced preferred orientations, ...Cryo-electron microscopy (cryo-EM) has become a powerful tool to resolve high-resolution structures of biomacromolecules in solution. However, air-water interface induced preferred orientations, dissociation or denaturation of biomacromolecules during cryo-vitrification remains a limiting factor for many specimens. To solve this bottleneck, we developed a cryo-EM support film using 2D crystals of hydrophobin HFBI. The hydrophilic side of the HFBI film adsorbs protein particles via electrostatic interactions and sequesters them from the air-water interface, allowing the formation of sufficiently thin ice for high-quality data collection. The particle orientation distribution can be regulated by adjusting the buffer pH. Using this support, we determined the cryo-EM structures of catalase (2.29 Å) and influenza haemagglutinin trimer (2.56 Å), which exhibited strong preferred orientations using a conventional cryo-vitrification protocol. We further show that the HFBI film is suitable to obtain high-resolution structures of small proteins, including aldolase (150 kDa, 3.28 Å) and haemoglobin (64 kDa, 3.6 Å). Our work suggests that HFBI films may have broad future applications in increasing the success rate and efficiency of cryo-EM. | ||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7vd8.cif.gz | 894.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vd8.ent.gz | 749.7 KB | Display | PDB format |
PDBx/mmJSON format | 7vd8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7vd8_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7vd8_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7vd8_validation.xml.gz | 114.7 KB | Display | |
Data in CIF | 7vd8_validation.cif.gz | 186.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vd/7vd8 ftp://data.pdbj.org/pub/pdb/validation_reports/vd/7vd8 | HTTPS FTP |
-Related structure data
Related structure data | 31910MC 7vd9C 7vdaC 7vdcC 7vdeC 7vdfC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 20116.547 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 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P02794, ferroxidase #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-NA / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Human apoferritin / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT | ||||||||||||
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Molecular weight | Value: 0.48 MDa / Experimental value: NO | ||||||||||||
Source (natural) | Organism: Homo sapiens (human) | ||||||||||||
Source (recombinant) | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) | ||||||||||||
Buffer solution | pH: 6.5 | ||||||||||||
Buffer component |
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Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||
Specimen support | Grid material: NICKEL/TITANIUM / Grid mesh size: 300 divisions/in. | ||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 165000 X |
Image recording | Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of real images: 2649 |
Image scans | Movie frames/image: 32 |
-Processing
Software | Name: PHENIX / Version: dev_4206: / Classification: refinement | ||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 351565 | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: O (octahedral) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 1.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 108183 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
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