What is mpstruc?

mpstruc is a manually curated database of membrane proteins, whose structures are deposited in the PDB. In this classification, membrane associated protein entities are organized into three levels:

• Group - focuses on the way in which the protein interacts with membranes - e.g., associated on only one side of the bilayer membrane (monotopic) or transmembrane regions which are either alpha-helical or beta barrels
• Subgroup - focuses on organizing proteins by their functions and taxonomy
• Protein - are defined at the level of individual PDB structures, within the subgroup

Note that the classification includes structures of the same protein derived from different source organisms (e.g., human, bacterial, yeast). Mutants of the protein are not included in the resource.

See also the membrane protein resources page for general information and a comparison to the OPM tree that also provides annotations of membrane proteins.

Why browse by mpstruc classification?

Proteins with similar membrane-related characteristics (like integral or peripheral proteins) have similar sequence, structural, and/or functional features. Browsing through the mpstruc browser tree can help users find polymer entities in the PDB that are membrane proteins, and explain their structural and functional relationships.

How to use the mpstruc Browser?

Users can click on the browser tree branches to navigate to a group of membrane proteins, or search for polymer entities with a particular classification by typing in the ‘Group’/’Subgroup’/’Protein’ names in the search box on the page. Users can view the corresponding number of PDB polymer entities that match the search term by clicking on the numbers listed next to the ‘Group’, ‘Subgroup’, or ‘Protein’ name will launch a search for all structures in the PDB that share this classification.

Examples

• Structures of photosystems can be identified in 2 ways:
• Browse the tree for “TRANSMEMBRANE PROTEINS: ALPHA-HELICAL” > “Photosystems” (additional subcategories are provided)
• Search by typing “photosystem” in the search box on the page and select from the options provided
• Structures of GLP-1 receptor can be identified by typing in “GLP-1” in the search box on the page and selecting from options provided