JCVI-syn3A Minimal Cell
Collagen and Extracellular Matrix
Escherichia coli Bacterium
Myoglobin in a Whale Muscle Cell
Cellulose Synthase
CytoSkeleton
Transfer RNA and Gag Protein
RecA and DNA
Casein Micelle and Fat Globule in Milk
Model of a Mycoplasma Cell
Myelin
Immunological Synapse
SARS-CoV-2 Fusion
Red Blood Cell Cytoskeleton
SARS-CoV-2 and Neutralizing Antibodies
Respiratory Droplet
Coronavirus
SARS-CoV-2 mRNA Vaccine
Coronavirus Life Cycle
Influenza Vaccine
Measles Virus Proteins
Lipid Droplets
Poliovirus Neutralization
Excitatory and Inhibitory Synapses
Abiogenesis
Last Universal Common Ancestor
Zika Virus
Insulin Action
Ebola Virus
Mycoplasma mycoides
Chloroplast
Autophagy
Vascular Endothelial Growth Factor (VegF) Signaling
Biosites: Muscle
Biosites: Basement Membrane
Biosites: Red Blood Cell
Biosites: Nucleus
Biosites: Blood Plasma
Biosites: Cytoplasm
Blood
Escherichia coli
HIV in Blood Plasma

Molecular Landscapes by David S. Goodsell

Model of a Mycoplasma Cell, 2021

Acknowledgement: Martina Maritan, Ludovic Autin, David S. Goodsell, Scripps Research and RCSB Protein Data Bank. doi: 10.2210/rcsb_pdb/goodsell-gallery-040

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).

Detailed descriptions of the data curation, model building, and visualization methods can be found in the Journal of Molecular Graphics article: ‘Building Structural Models of a Whole Mycoplasma Cell’, https://doi.org/10.1016/j.jmb.2021.167351. Additional images of this model are available at the Center for Computational Structural Biology at Scripps Research.