Published quarterly by the Research Collaboratory for Structural Bioinformatics Protein Data Bank

Message from RCSB PDB

Last Fall, the RCSB PDB Newsletter highlighted Structural Biology Pipeline Meets the High School Classroom. For this feature, Biology Teacher Dan Williams coordinated articles from the point of view of students and of teachers from Long Island, NY involved in SPARK (Students Partnerships for Advance Research and Knowledge), a collaborative program by the Office of Educational Programs and NSLS-II at Brookhaven National Laboratory (BNL).

With this week’s update of the PDB, the first structure from this program, a methylenetetrahydrofolate reductase (MTHFR) was made publicly available as PDB entry 6PEY.

Shelter Island students Emma Gallagher and Lauren Gurney worked in collaboration with students from across Long Island to perform hundreds of crystallization reactions, freeze the MTHFR crystals in liquid nitrogen, and obtain X-ray diffraction data using the AMX beamline at Brookhaven National Laboratory’s National Synchrotron Light Source II. Countless hours were spent analyzing the data using standard structural biology programs such as CCP4 and COOT.

Left: PDB Structure 6pey. Right: SPARK students working in COOT.

MTHFR has been implicated in many human diseases including but not limited to cardiovascular disease and miscarriage. It is hoped that further examination of this structure will help scientists, like these students, understand how MTHFR works and lead to better treatments.

Thanks to the SPARK program, high school students like Emma and Lauren and hundreds of other Long Islanders have joined the worldwide PDB Data Depositors community. Soon, other PDB structures from this program will be released. By working together, all of the students in the SPARK program have helped make each other to be better scientists.

This achievement was made possible by the continuous guidance and support of the scientists in BNL’s SPARK program and Office of Educational Programs, Dr. Aleida Perez, Dr. Alexei Soares, and Dr. Vivian Stojanoff.

For more, see Structural Biology Pipeline Meets the High School Classroom.

Mural at Shelter Island High School inspired by the SPARK program and the RCSB PDB-ACA Coloring Book.

Snapshot: October 1, 2019
156,365 Released atomic coordinate entries
Molecule Type
144,967 Proteins, peptides, and viruses
3,389 Nucleic acids
7,979 Protein/nucleic acid complexes
30 Other
Experimental Technique
139,341 X-ray
12,775 NMR
3,799 Electron Microscopy
152 Hybrid
298 Other
Related Experimental Data Files
129,252 Structure factors
10,125 NMR restraints
3,877 Chemical shifts
3,876 3DEM map files