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- PDB-8aey: 3 A CRYO-EM STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS FERRITIN FROM... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8aey | |||||||||
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Title | 3 A CRYO-EM STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS FERRITIN FROM TIMEPIX3 detector | |||||||||
![]() | Ferritin BfrB | |||||||||
![]() | METAL TRANSPORT / IRON STORAGE / FERROXIDASE / BACTERIAL FERRITIN / OCTAHEDRAL SYMMETRY. | |||||||||
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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.05 Å | |||||||||
![]() | Zhang, Y. / van Schayck, J.P. / Knoops, K. / Peters, P.J. / Ravelli, R.B.G. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Integration of an Event-driven Timepix3 Hybrid Pixel Detector into a Cryo-EM Workflow Authors: van Schayck, J.P. / Zhang, Y. / Knoops, K. / Peters, P.J. / Ravelli, R.B.G. #1: ![]() 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
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 807 KB | Display | ![]() |
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PDB format | ![]() | 671.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 113.6 KB | Display | |
Data in CIF | ![]() | 137.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 15389MC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 20463.936 Da / Num. of mol.: 24 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: bfrB / Plasmid: PRSET / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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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: MYCOBACTERIUM TUBERCULOSIS FERRITIN / Type: COMPLEX / Details: MYCOBACTERIUM TUBERCULOSIS FERRITIN / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 8 |
Specimen | Conc.: 40 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI ARCTICA Details: BASIC DIRECT ALIGNMENTS WERE DONE AS WELL AS ASTIGMATISM AND COMA ALIGNMENT USING AUTOCTF |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 215000 X / Nominal defocus max: 1400 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 1.5 sec. / Electron dose: 50 e/Å2 / Film or detector model: OTHER / Num. of real images: 2977 |
Image scans | Sampling size: 55 µm / Width: 512 / Height: 512 |
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Processing
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EM software |
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Image processing |
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CTF correction |
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Particle selection |
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Symmetry |
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3D reconstruction | Algorithm: FOURIER SPACE / Entry-ID: 8AEY / Num. of particles: 11422 / Resolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Symmetry type: POINT
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Atomic model building | B value: 79.7 / Protocol: OTHER / Space: REAL / Target criteria: CORRELATION COEFFICIENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 7O6E Pdb chain-ID: A | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 80.21 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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