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Yorodumi- EMDB-9915: Cryo-EM structure of Holo-bacterioferritin form-II from Streptomy... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9915 | |||||||||
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Title | Cryo-EM structure of Holo-bacterioferritin form-II from Streptomyces coelicolor | |||||||||
Map data | Cryo_EM map of bacterioferritin from Streptomyces coelicolor form II | |||||||||
Sample |
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Keywords | Ferritin / Nanocage / Bacterioferritin / METAL TRANSPORT | |||||||||
Function / homology | Function and homology information ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / iron ion transport / iron ion binding / heme binding / cytosol Similarity search - Function | |||||||||
Biological species | Streptomyces coelicolor (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.5 Å | |||||||||
Authors | Jobichen C / Sivaraman J | |||||||||
Citation | Journal: To Be Published Title: Cryo-EM structure of Bacterioferritin from Streptomyces coelicolor Authors: Jobichen C / Sivaraman J | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_9915.map.gz | 48.8 MB | EMDB map data format | |
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Header (meta data) | emd-9915-v30.xml emd-9915.xml | 11 KB 11 KB | Display Display | EMDB header |
Images | emd_9915.png | 81.1 KB | ||
Filedesc metadata | emd-9915.cif.gz | 5.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9915 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9915 | HTTPS FTP |
-Validation report
Summary document | emd_9915_validation.pdf.gz | 528.5 KB | Display | EMDB validaton report |
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Full document | emd_9915_full_validation.pdf.gz | 528.1 KB | Display | |
Data in XML | emd_9915_validation.xml.gz | 6.4 KB | Display | |
Data in CIF | emd_9915_validation.cif.gz | 7.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9915 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9915 | HTTPS FTP |
-Related structure data
Related structure data | 6k4mMC 9910C 9913C 6k3oC 6k43C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_9915.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo_EM map of bacterioferritin from Streptomyces coelicolor form II | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Bacterioferritin in complex with HEME and IRON
Entire | Name: Bacterioferritin in complex with HEME and IRON |
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Components |
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-Supramolecule #1: Bacterioferritin in complex with HEME and IRON
Supramolecule | Name: Bacterioferritin in complex with HEME and IRON / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Streptomyces coelicolor (bacteria) |
Molecular weight | Theoretical: 500 KDa |
-Macromolecule #1: Bacterioferritin
Macromolecule | Name: Bacterioferritin / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO / EC number: ferroxidase |
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Source (natural) | Organism: Streptomyces coelicolor (bacteria) |
Molecular weight | Theoretical: 19.242629 KDa |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Sequence | String: MQGDPEVIEF LNEQLTAELT AINQYFLHAK LQDHKGWTKL AKYTRAESFD EMRHAEVLTD RILLLDGLPN YQRLFHVRVG QSVTEMFQA DREVELEAID RLRRGIEVMR AKHDITSANV FEAILADEEH HIDYLETQLD LIEKLGESLY LSTVIEQTQP D PSGPGSL UniProtKB: Bacterioferritin |
-Macromolecule #2: FE (II) ION
Macromolecule | Name: FE (II) ION / type: ligand / ID: 2 / Number of copies: 24 / Formula: FE2 |
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Molecular weight | Theoretical: 55.845 Da |
-Macromolecule #3: PROTOPORPHYRIN IX CONTAINING FE
Macromolecule | Name: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 3 / Number of copies: 12 / Formula: HEM |
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Molecular weight | Theoretical: 616.487 Da |
Chemical component information | ChemComp-HEM: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.8 mg/mL |
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Buffer | pH: 7 |
Vitrification | Cryogen name: ETHANE |
Details | This sample was monodisperse with 24mer nanocage assemblies. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 1.6 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 2.7 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
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 | Applied symmetry - Point group: O (octahedral) / Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM / Number images used: 13793 |
Initial angle assignment | Type: RANDOM ASSIGNMENT / Software - Name: cisTEM |
Final angle assignment | Type: ANGULAR RECONSTITUTION / Software - Name: cisTEM |