What are Source Organisms?

A majority of biopolymers whose structures are deposited in the PDB are human, bacterial, yeast, or plant specific (e.g., spinach) proteins, nucleic acids, or carbohydrates. The organism from which the protein or nucleotide etc. is originally derived is called the source organism.

In some cases these proteins and nucleic acids are purified directly from the cells/tissues of the source organisms. However, frequently the genes of the proteins being studied are cloned and expressed in another organism, - e.g., the gene of a human protein is cloned, introduced into bacteria, and expressed there. The protein still remains a human protein that is expressed in a bacterial host or expression system. This approach allows researchers to produce sufficient quantities of the protein of interest for the experiment and also enables them to make small changes in the protein/nucleic acid to examine its impact on structure and function of the biopolymer.

Note: Some proteins/nucleic acids in the PDB may be designed molecules and not have a specific source organism.

What is the Source Organism Browser?

The Source Organism browser is a hierarchical representation of all organisms in the NCBI Taxonomy database (Taxonomy). For polymer entities in the PDB source organism assignment is based on author provided information, and UniProtKB, or NCBI GenBank specified mapping of the source organism. All PDB structures that have a source organism are included in this browser tree.

Why Browse by Source Organism?

Browsing through this tree can help view the number of polymer entities in the PDB that have proteins or nucleic acids derived from that source. So when searching for a protein or nucleic acid (DNA/RNA) from a specific organism you can begin from this browser tree.

How to use the Source Organism Browser?

Users can browse the taxonomy tree, by typing in an organism scientific name in the search box at the top of the page. In addition, the common name, scientific name, or taxonomy ID of an organism can be used to search in the browser.

After locating the organism of interest in the browser tree, view the number of polymer entities (proteins/nucleic acids etc.) included in this group. Clicking on the numbers listed next to the organism name will launch a search for all polymer entities in the PDB that are associated with that source organism.

Example

Search for the structures of all rabbit proteins and nucleic acids can be done as follows:

• Type in the common name of the organism in the search box on the page and select from the options “rabbit” >> “Oryctolagus cuniculus (domestic rabbit) (9986)”.
• If the complete scientific name and/or taxonomy ID of the organism is known, type that into the search box. e.g., “Oryctolagus cuniculus” or “9986” and select from options provided.