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Explore Protein Modifications

07/05

Proteins are modified at different stages of protein synthesis, including pre-translational (i.e., N-formylation), co-translational, and post-translational modifications.

Protein Modifications in the PDB have been mapped to the RESID database of Protein Modifications (J.S. Garavelli, Nucl. Acids Res. (2003), 31, 499-501) and the associated Protein Modifications Ontology PSI-MOD (L. Montecchi-Palazzi, et al., Nat. Biotech (2008), 26, 864-866).

Below, we describe how to browse, search, and visualize protein modifications.

Tree Browser

Protein modifications can be browsed by two PSI-Mod Ontologies, categorized by either the amino acid involved in the modification or by the chemical process involved in the formation.

The Protein Modification Browser can be accessed by clicking on the "Browse by Annotations" link under the text search box on the home page. The tree browser hierarchy can be expanded by clicking on the triangles or by typing in text in the autocomplete search box. For each branch of the tree hierarchy, the number of PDB structures that contain the modification is displayed and is linked to the search results page.

RCSB PDB News ImageProtein Modification Tree Browser

Advanced Search

A "Protein Modification" search has been added to the Advanced Search under the "Sequence Feature" category.

RCSB PDB News ImageAdvanced Search menu

Protein Modifications can be searched by the modification name, keyword, RESID ID, PSI-MOD ID, and the wwPDB Chemical Component ID.

RCSB PDB News ImageProtein Modification Advanced Search Options

Protein Modification Track on Sequence tab

The Sequence tab option on Structure Summary pages visually maps an entry’s sequence with structural annotations. A new annotation protein modification is now available. The type of modification and links to the RESID database and the PSI-MOD ontology are given in the text box on the left. The color code in the annotations box is used to highlight the modification on the sequence display. In addition, a legend on the bottom explains the symbols and colors used for each modification.

RCSB PDB News ImageProtein Modification Track on Sequence tab (Example PDB ID 5EVB shows a hexacoordinated zinc ion and an L-cystine cross-link). The shape of the symbol indicates the number of residues involved in a cross-link (e.g., vertical bar: between two residues, hexagon: hexacoordinated group). The lines link the cross-linked residues.

Visualize Protein Modifications in 3D

The JSmol 3D view page, available from an entry’s Structure Summary page, offers special tools for viewing ligand interactions and protein domains. The ability to view specific protein modifications in 3D has been added to these options. To access this view, scroll down to the bottom of the 3D View page and select the “Modification” tab. Selecting a feature listed in the “type” column will highlight the modification in the 3D viewer above.

RCSB PDB News ImageJSmol visualization of protein modifications (Example PDB ID 5EVB with L-cystine modification selected in the Modification tab of the JSmol page).