Happy anniversary, PDBe!
Happy anniversary, PDBe!
Nowadays, we can see the position of atoms as if we had vision millions of times sharper than human eyes allow. This is the gift of structural biology – the science of figuring out the three-dimensional structures of molecules (usually proteins), and correlating their shape to their function. Such insights give us clues about how changing a molecule’s shape could change what it does. That’s essentially how medicines work.
Determining the shapes of molecules is painstaking work, so sharing that knowledge openly with scientists around the world is essential for publicly funded research to proceed efficiently. EMBL-EBI is at the heart of open data in the life sciences, and hosts the European arm of the world’s longest-running molecular data resource: the Protein Data Bank (PDB). Launched in 1971, the PDB is now a worldwide collaboration (wwPDB) hosting databases in the US, Japan and Europe that inspire innovation and promote understanding of the fundamental processes of life.
As the Protein Data Bank in Europe (PDBe) looks back on its 20th year in operation - and celebrates its annotation of the PDB's 25,000th structure today - Ewan Birney is marking its success by paying homage to some of its most intriguing tenants.
Which structures made the grade?
The first of Birney’s nine ‘Structures of Christmas’ is lysozyme, a protein found in our tears (and egg whites). It is one of the most researched protein structures, and was the first enzyme structure to be solved via X-ray diffraction.
The rest of Birney's Structures of Christmas include:
- A machine that makes machines
- A protein that lets us see light
- An entity that causes a hideous disease in cattle
- An inefficient molecule that led to the evolution of plants
- A killer of human gut cells that tricks a human protein into helping it
- A sophisticated tool vertebrates use to defend themselves, which employs a deliberate randomisation strategy
- A major player in giving a cell its shape and making cells move
- A structure that helps break down lactose to galactose and glucose, and was determined at very high resolution using cryo-Electron Microscopy.
Photo: Thanks to the curators in our Protein Data Bank in Europe team who helped us create eight 3D structures as ornaments on the EMBL-EBI Christmas tree! Lysozyme was too fiddly to print, but the rest worked out beautifully. Special thanks to Matthew Conroy and Alice Clark for their help. Pictured from left to right: Eduardo Sanz-Garcia, Abhik Mukhopadhyay, Typhaine Paysan-Lafosse, David Armstrong, Matthew Conroy, John Berrisford, Sanja Abbott, Lora Mak, Andrii Iudin, Alice Clark, Oliver Smart and Carlos Lugo. [“Christmas structures” 3D print design and photo credit: Spencer Phillips, EMBL-EBI]