Molecular Landscapes

02/15 PDB101 News

This image shows a 3D model of an entire Mycoplasma genitalium cell. This snapshot represents a Mycoplasma cell at the beginning of its life cycle. Cell shape has been approximated to a sphere with a radius of ~145nm. Each protein is represented by a 3D structure coming from either homology modeling, a previous model of mycoplasma cytoplasm, experimental data, or homologs from the Protein Data Bank. The nucleoid structure was modeled with LatticeNucleoid. Small molecules, ions, and water are not shown in the illustration, and would fill the spaces between the macromolecules.

In the image, two clipping planes progressively hide parts of the model. The upper section highlights ribosomes (magenta), DNA (yellow) and mRNA (pink) filaments; the central section shows the bacterial nucleoid in the context of soluble macromolecules (DNA-binding proteins in orange, cytoplasmic proteins in shades of blue, tRNAs in bright pink); the lower section shows the cell membrane (grey/green) with associated membrane proteins (shades of green). Additional images of this model are available at the Center for Computational Structural Biology at Scripps Research.

For detailed descriptions of the data curation, model building, and visualization methods, see:
Building Structural Models of a Whole Mycoplasma Cell
(2022) Journal of Molecular Graphics 434: 167351 doi: 10.1016/j.jmb.2021.167351.

This model is part of PDB-101's SciArt gallery of Molecular Landscapes by David S. Goodsell.

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