Protein structures are used to understand the architecture
of a protein, to explain how a protein interacts with its ligands or cofactors
and to study the composition of protein complexes. They help us to identify the
position and nature of post-translational modifications and, as 3D structure is
more evolutionarily conserved than primary sequence, can also be used to predict
protein function. Identifying proteins sharing a conserved protein fold may help
to also ascertain a molecular function that is common to them all. Understanding
how topology affects the active sites of enzymes or identifying sequence-conserved
regions, such as binding sites or areas of electrostatic potential, on the
surface of a protein can also give valuable clues to the role a protein plays
in a cell.
Annotation of proteins based on structure-based analyses is
an integral part of the work of the UniProt Knowledgebase (UniProtKB). UniProt
works closely with the Protein Databank in Europe (PDBe) to map 3D structural
entries (~100,000) to the appropriate UniProtKB entries at the individual
residue level [1]. It then becomes possible to use the UniProtKB advanced
search functionality to ask questions such as ‘How many proteins in the human
proteome have at least a partial 3D structure?’
Searching for structural data in UniProtKB
Once you have found the protein you are interested in, use
our navigation tool in the entry to move to the Structure section where you may
either find more information in the table view or visualise a 3D image. The
table view lists all the structures available for that molecule, give details
of the method by which the structure has been determined (e.g. X-ray, NMR,
Electron Microscopy) and an accurate residue-level mapping to the region of
amino acid sequence covered by each structure. Links to a number of external
data repositories and resources enable you to access more detailed information.
To help our users visualize the
structure, we have recently incorporated the LiteMol Viewer, an HTML5 web
application that not only provides cartoons, surface and balls and stick
visualizations but also links you to the PDBe database, allowing you to view
and explore validation and annotation data.
Visualising Bloom's syndrome helicase (P54132)
in complex with ADP and duplex DNA.
Hovering over the structure will show you the amino-acid
residue-level mappings, a single click and you can zoom in to a more detailed
view, for example enabling you to visualize the details of cofactor binding.
Zooming in on Bloom's syndrome helicase to show ADP binding
Knowing the shape of a protein can give you valuable clues
to the function of that molecule. Use UniProtKB to explore the links between
sequence, structure and function and understand how molecule topology can drive
cellular phenotype.
Want to learn more:
Go to our pre-recorded webinars to learn more about the annotation of structural data in UniProtKB
