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Open data
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Basic information
| Entry | Database: PDB / ID: 9sjv | |||||||||||||||||||||||||||||||||||||||
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| Title | Cryo-EM structure of Human Apoferritin at pH 9 | |||||||||||||||||||||||||||||||||||||||
Components | Ferritin heavy chain, N-terminally processed | |||||||||||||||||||||||||||||||||||||||
Keywords | METAL BINDING PROTEIN / Apoferritin / Ferritin / Metal storage / Low pH | |||||||||||||||||||||||||||||||||||||||
| Function / homology | Function and homology informationiron ion sequestering activity / ferritin complex / Scavenging by Class A Receptors / negative regulation of ferroptosis / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding ...iron ion sequestering activity / ferritin complex / Scavenging by Class A Receptors / negative regulation of ferroptosis / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding / autophagosome / iron ion transport / ferrous iron binding / Iron uptake and transport / tertiary granule lumen / ficolin-1-rich granule lumen / intracellular iron ion homeostasis / immune response / iron ion binding / negative regulation of cell population proliferation / Neutrophil degranulation / extracellular exosome / extracellular region / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||||||||||||||||||||||||||||||||
| Biological species | Homo sapiens (human) | |||||||||||||||||||||||||||||||||||||||
| Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.89 Å | |||||||||||||||||||||||||||||||||||||||
Authors | Skalidis, I. / Semchonok, D.A. / Tueting, C. / Hamdi, F. / Kastritis, P.L. | |||||||||||||||||||||||||||||||||||||||
| Funding support | European Union, Germany, Portugal, 12items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2026Title: Direct evidence of acid-driven protein desolvation Authors: Hamdi, F. / Skalidis, I. / Schwerin, I.K. / Belapure, J. / Semchonok, D.A. / Kyrilis, F.L. / Tueting, C. / Mueller, J. / Kuenze, G. / Kastritis, P.L. | |||||||||||||||||||||||||||||||||||||||
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 9sjv.cif.gz | 816.5 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb9sjv.ent.gz | 682.2 KB | Display | PDB format |
| PDBx/mmJSON format | 9sjv.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sj/9sjv ftp://data.pdbj.org/pub/pdb/validation_reports/sj/9sjv | HTTPS FTP |
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-Related structure data
| Related structure data | ![]() 54955MC ![]() 9sjrC ![]() 9sjsC ![]() 9sjtC ![]() 9sjuC M: map data used to model this data C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
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Assembly
| Deposited unit | ![]()
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Components
| #1: Protein | Mass: 20176.600 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, PIG15Production host: ![]() References: UniProt: P02794 #2: Chemical | ChemComp-FE / #3: Chemical | ChemComp-MG / #4: Water | ChemComp-HOH / | Has ligand of interest | N | Has protein modification | 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 |
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Sample preparation
| Component | Name: 24-mer of Human Apoferritin at pH 9 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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| Molecular weight | Value: 0.5 MDa / Experimental value: NO |
| Source (natural) | Organism: Homo sapiens (human) |
| Source (recombinant) | Organism: ![]() Plasmid: LF2422 |
| Buffer solution | pH: 9 |
| Specimen | Conc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
| Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1 |
| Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
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Electron microscopy imaging
| Microscopy | Model: TFS GLACIOS |
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| Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN |
| Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
| Specimen holder | Cryogen: NITROGEN |
| Image recording | Electron dose: 30 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 1867 |
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Processing
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| CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||
| Particle selection | Num. of particles selected: 438640 | ||||||||||||||||||||||||||||||||||||||||||||
| Symmetry | Point symmetry: O (octahedral) | ||||||||||||||||||||||||||||||||||||||||||||
| 3D reconstruction | Resolution: 1.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 343262 / Algorithm: SIMULTANEOUS ITERATIVE (SIRT) / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
| Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||
| Atomic model building | Details: UniProt ID: P02794 / Source name: Other / Type: experimental model |
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About Yorodumi




Homo sapiens (human)
Germany,
Portugal, 12items
Citation








PDBj








FIELD EMISSION GUN