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Yorodumi- PDB-8cu8: Cryo-EM structure of Ferritin 2 from Caenorhabditis elegans, FTN-2 -
+Open data
-Basic information
Entry | Database: PDB / ID: 8cu8 | ||||||
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Title | Cryo-EM structure of Ferritin 2 from Caenorhabditis elegans, FTN-2 | ||||||
Components | Ferritin | ||||||
Keywords | OXIDOREDUCTASE / ferroxidase | ||||||
Function / homology | Function and homology information Iron uptake and transport / Neutrophil degranulation / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / ferrous iron binding / iron ion transport / defense response to Gram-positive bacterium / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Caenorhabditis elegans (invertebrata) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.91 Å | ||||||
Authors | Malcolm, T.R. / Brown, H.G. / Hanssen, E. | ||||||
Funding support | Australia, 1items
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Citation | Journal: To Be Published Title: Biochemical Characterization of Caenorhabditis elegans Ferritins Authors: Mubarak, S.M.M. / Malcolm, T.R. / Brown, H.G. / Hanssen, E. / Maher, M.J. / McColl, G. / Jameson, G.N.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8cu8.cif.gz | 736.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cu8.ent.gz | 617.5 KB | Display | PDB format |
PDBx/mmJSON format | 8cu8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8cu8_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8cu8_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8cu8_validation.xml.gz | 91.7 KB | Display | |
Data in CIF | 8cu8_validation.cif.gz | 137.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cu/8cu8 ftp://data.pdbj.org/pub/pdb/validation_reports/cu/8cu8 | HTTPS FTP |
-Related structure data
Related structure data | 26996MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 19371.547 Da / Num. of mol.: 24 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: ftn-2, CELE_D1037.3, D1037.3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9TYS3, ferroxidase #2: Chemical | ChemComp-FE / #3: 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: Homo 24-mer of Ferritin 2 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: Caenorhabditis elegans (invertebrata) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid type: UltrAuFoil R1.2/1.3 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1400 nm / Nominal defocus min: 600 nm |
Image recording | Electron dose: 47.6 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 1.91 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 398769 / Symmetry type: POINT |