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Yorodumi- EMDB-26996: Cryo-EM structure of Ferritin 2 from Caenorhabditis elegans, FTN-2 -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26996 | |||||||||
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Title | Cryo-EM structure of Ferritin 2 from Caenorhabditis elegans, FTN-2 | |||||||||
Map data | Ferritin 2 from Caenorhabditis elegans, FTN-2 | |||||||||
Sample |
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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 | single particle reconstruction / cryo EM / Resolution: 1.91 Å | |||||||||
Authors | Malcolm TR / Brown HG / Hanssen E | |||||||||
Funding support | Australia, 1 items
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Citation | Journal: To Be Published Title: Biochemical Characterization of Caenorhabditis elegans Ferritins Authors: Mubarak SMM / Malcolm TR / Brown HG / Hanssen E / Maher MJ / McColl G / Jameson GNL | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_26996.map.gz | 67.9 MB | EMDB map data format | |
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Header (meta data) | emd-26996-v30.xml emd-26996.xml | 13.8 KB 13.8 KB | Display Display | EMDB header |
Images | emd_26996.png | 89.1 KB | ||
Filedesc metadata | emd-26996.cif.gz | 5.1 KB | ||
Others | emd_26996_half_map_1.map.gz emd_26996_half_map_2.map.gz | 124.6 MB 124.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26996 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26996 | HTTPS FTP |
-Validation report
Summary document | emd_26996_validation.pdf.gz | 867 KB | Display | EMDB validaton report |
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Full document | emd_26996_full_validation.pdf.gz | 866.5 KB | Display | |
Data in XML | emd_26996_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | emd_26996_validation.cif.gz | 16.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26996 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26996 | HTTPS FTP |
-Related structure data
Related structure data | 8cu8MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_26996.map.gz / Format: CCP4 / Size: 134.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Ferritin 2 from Caenorhabditis elegans, FTN-2 | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.82 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Ferritin 2 from Caenorhabditis elegans, FTN-2
File | emd_26996_half_map_1.map | ||||||||||||
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Annotation | Ferritin 2 from Caenorhabditis elegans, FTN-2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Ferritin 2 from Caenorhabditis elegans, FTN-2
File | emd_26996_half_map_2.map | ||||||||||||
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Annotation | Ferritin 2 from Caenorhabditis elegans, FTN-2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Homo 24-mer of Ferritin 2
Entire | Name: Homo 24-mer of Ferritin 2 |
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Components |
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-Supramolecule #1: Homo 24-mer of Ferritin 2
Supramolecule | Name: Homo 24-mer of Ferritin 2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Caenorhabditis elegans (invertebrata) |
-Macromolecule #1: Ferritin
Macromolecule | Name: Ferritin / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO / EC number: ferroxidase |
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Source (natural) | Organism: Caenorhabditis elegans (invertebrata) |
Molecular weight | Theoretical: 19.371547 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: SLARQNYHSE VEAAVNKQIN IELYASYVYL SMSFYFDRDD VALPNIAKFF KEQSDEEREH ATELMRVQNL RGGRVVLQDI QKPENDEWG TALKAFEAAL ALEKFNNESL LKLHSTAGNH NDAHLTDFIE EKYLDEQVKS INEFARMVAN LKRVGPGVGE Y VFDKEHFS UniProtKB: Ferritin |
-Macromolecule #2: FE (III) ION
Macromolecule | Name: FE (III) ION / type: ligand / ID: 2 / Number of copies: 24 / Formula: FE |
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Molecular weight | Theoretical: 55.845 Da |
-Macromolecule #3: water
Macromolecule | Name: water / type: ligand / ID: 3 / Number of copies: 2271 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 47.6 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.4000000000000001 µm / Nominal defocus min: 0.6 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 1.91 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 398769 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |