Adapted from the ALS Passes 7,000-Protein Milestone article on May 30, 2018
Today, the nine structural biology beamlines at the ALS passed a major milestone of collectively depositing over 10,000 protein structures into the Protein Data Bank (PDB), a worldwide, open-access repository of protein structures.
With this achievement, the ALS continues to play a key role in advancing research on global health challenges—from malaria and COVID-19 to cancer. ALS-derived structures have also supported two recent Nobel Prize-winning breakthroughs: the development of gene editing tools and the computational design of de novo proteins.
Partnerships across the world converging at the ALS made this accomplishment possible. ALS participating research teams, including many researchers from the Biosciences Area of Berkeley Lab and Molecular Biology Consortium, work with users from both academia and industry to conduct experiments at the ALS beamlines to determine the structures of proteins and better understand their biological functions. The users then deposit these structures into the PDB.
“In collaboration with my users through the Collaborative Crystallography program, I’m proud to be part of the effort that has deposited 500 protein structures into the PDB,” said Banu Sankaran, a crystallographer and research scientist in the Molecular Biophysics and Integrated Bioimaging Division.
Although the ALS is primarily a soft x-ray facility, its long-standing support for a hard x-ray structural biology program makes this milestone particularly noteworthy.
The ALS’s structural biology program began in 1997 with the launch of Beamline 5.0.2, powered by a wiggler insertion device for generating hard x-rays. The first ALS-derived protein structure was deposited in the PDB in 1998. The program quickly expanded with Beamlines 5.0.1 and 5.0.3, followed by superbend beamlines—4.2.2, 8.2.1, 8.2.2, 8.3.1, and 12.3.1—beginning in the early 2000s. Additionally, the state-of-the-art microfocus Beamline 2.0.1 (GEMINI) is fully autonomous and deposited its first structure in 2023.
The PDB, founded in 1971 at Brookhaven National Laboratory with just seven entries, now holds over 220,000 structures and serves as a vital resource for biological research and drug discovery worldwide—an effort in which the ALS is proud to participate.