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- EMDB-15389: 3 A CRYO-EM STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS FERRITIN FROM... -
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Basic information
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Title | 3 A CRYO-EM STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS FERRITIN FROM TIMEPIX3 detector | |||||||||
![]() | The map is sharpened by Locspiral. | |||||||||
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![]() | IRON STORAGE / FERROXIDASE / BACTERIAL FERRITIN / OCTAHEDRAL SYMMETRY. / METAL TRANSPORT | |||||||||
Function / homology | ![]() Mtb iron assimilation by chelation / response to nitrosative stress / encapsulin nanocompartment / iron ion sequestering activity / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / peptidoglycan-based cell wall / ferric iron binding / ferrous iron binding ...Mtb iron assimilation by chelation / response to nitrosative stress / encapsulin nanocompartment / iron ion sequestering activity / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / peptidoglycan-based cell wall / ferric iron binding / ferrous iron binding / iron ion transport / response to hypoxia / extracellular region / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.05 Å | |||||||||
![]() | Zhang Y / van Schayck JP / Knoops K / Peters PJ / Ravelli RBG | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Mycobacterium tuberculosis ferritin: a suitable workhorse protein for cryo-EM development. Authors: Abril Gijsbers / Yue Zhang / Ye Gao / Peter J Peters / Raimond B G Ravelli / ![]() Abstract: The use of cryo-EM continues to expand worldwide and calls for good-quality standard proteins with simple protocols for their production. Here, a straightforward expression and purification protocol ...The use of cryo-EM continues to expand worldwide and calls for good-quality standard proteins with simple protocols for their production. Here, a straightforward expression and purification protocol is presented that provides an apoferritin, bacterioferritin B (BfrB), from Mycobacterium tuberculosis with high yield and purity. A 2.12 Å resolution cryo-EM structure of BfrB is reported, showing the typical cage-like oligomer constituting of 24 monomers related by 432 symmetry. However, it also contains a unique C-terminal extension (164-181), which loops into the cage region of the shell and provides extra stability to the protein. Part of this region was ambiguous in previous crystal structures but could be built within the cryo-EM map. These findings and this protocol could serve the growing cryo-EM community in characterizing and pushing the limits of their electron microscopes and workflows. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 37 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 22.7 KB 22.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 13.9 KB | Display | ![]() |
Images | ![]() | 81.1 KB | ||
Masks | ![]() | 229.8 MB | ![]() | |
Filedesc metadata | ![]() | 6.2 KB | ||
Others | ![]() ![]() ![]() | 214.8 MB 175.9 MB 175.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 916.9 KB | Display | ![]() |
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Full document | ![]() | 916.5 KB | Display | |
Data in XML | ![]() | 22 KB | Display | |
Data in CIF | ![]() | 28.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8aeyMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | The map is sharpened by Locspiral. | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.6 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Density Histograms |
-Additional map: The map is sharpened by Relion postprocessing.
File | emd_15389_additional_1.map | ||||||||||||
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Annotation | The map is sharpened by Relion postprocessing. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_15389_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_15389_half_map_2.map | ||||||||||||
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Density Histograms |
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Sample components
-Entire : MYCOBACTERIUM TUBERCULOSIS FERRITIN
Entire | Name: MYCOBACTERIUM TUBERCULOSIS FERRITIN |
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Components |
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-Supramolecule #1: MYCOBACTERIUM TUBERCULOSIS FERRITIN
Supramolecule | Name: MYCOBACTERIUM TUBERCULOSIS FERRITIN / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: MYCOBACTERIUM TUBERCULOSIS FERRITIN |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Ferritin BfrB
Macromolecule | Name: Ferritin BfrB / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO / EC number: ferroxidase |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 20.463936 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MTEYEGPKTK FHALMQEQIH NEFTAAQQYV AIAVYFDSED LPQLAKHFYS QAVEERNHAM MLVQHLLDRD LRVEIPGVDT VRNQFDRPR EALALALDQE RTVTDQVGRL TAVARDEGDF LGEQFMQWFL QEQIEEVALM ATLVRVADRA GANLFELENF V AREVDVAP AASGAPHAAG GRL UniProtKB: Bacterioferritin BfrB |
-Macromolecule #2: water
Macromolecule | Name: water / type: ligand / ID: 2 / Number of copies: 240 / 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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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 40 mg/mL |
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Buffer | pH: 8 |
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 50 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TECNAI ARCTICA |
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Software | Name: SerialEM (ver. 4.0) |
Details | BASIC DIRECT ALIGNMENTS WERE DONE AS WELL AS ASTIGMATISM AND COMA ALIGNMENT USING AUTOCTF |
Image recording | Film or detector model: OTHER / Digitization - Dimensions - Width: 512 pixel / Digitization - Dimensions - Height: 512 pixel / Number real images: 2977 / Average exposure time: 1.5 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.4000000000000001 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 215000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Image processing #1
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Image processing #2
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Refinement | Space: REAL / Protocol: OTHER / Overall B value: 79.7 / Target criteria: CORRELATION COEFFICIENT |
Output model | ![]() PDB-8aey: |