RCSB Protein Data Bank Biocurator Joins Us Inside Nanome

Last week, Dr. Gregg Crichlow, Biocurator at the Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), joined us inside Nanome to look at two SARS-CoV-2 spike protein structures from the RCSB PDB.

Keita Funakawa
Nanome

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The RCSB PDB archive was established in 1971 to archive information about the 3D shapes of proteins, nucleic acids, and complex assemblies studied by structural biologists around the world. Today, millions of students and researchers use these freely-available data to help understand all aspects of biomedicine and agriculture, from protein synthesis to health and disease.

Structural biologists have focused on studying SARS-CoV-2 (the virus that causes COVID-19) structures during the pandemic. The first of these structures was released in the RCSB PDB archive on February 5, 2020–-less than one month after the virus genome sequence became public. Since then, hundreds of related entries have been deposited, carefully reviewed by biocurators like Dr. Crichlow, and then made rapidly available to the public [1].

At least 124 of the SARS-CoV-2–related entries deposited this year involve the spike protein.

Credit: Maria Voigt, RCSB PDB [2]

The spike protein plays a role in viral entry into host cells. Once the virus attaches to a cell via its spike protein, the viral membrane fuses with the cell’s membrane, enabling the virus to enter the cell and utilize the cell’s organelles and proteins to reproduce by making copies of its RNA genome.

Visualizing and understanding the 3D shapes of these biological macromolecules is vital to moving past this crisis.

PDB structures can be loaded into Nanome software for visualization and interrogation in virtual reality. In fact, the majority of our videos feature PDB structures.

In this video, Dr. Crichlow and our CEO, Steve McCloskey, examine a structure deposited by Benton et al. [3] and one by Barnes et al. [4]. The two papers describe key complexes that could help researchers identify and develop effective therapeutics: the spike protein bound to its receptor, angiotensin-converting enzyme 2 (ACE2), and the spike protein bound to antibodies.

Nanome software enables the 3D visualization of the interactions between the atoms in the complexes.

Watch the video to see how.

“A unified and publicly available database like the RCSB PDB didn’t exist during the spanish flu nor the bubonic plague … it enables scientists to move at unprecedented speeds,” said Dr. Crichlow.

Like Dr. Crichlow and his colleagues, we believe that knowing the 3D structure of a biological macromolecule is essential for understanding its role in human health and disease. And given SARS, MERS, and now SARS-CoV-2, it’s not unfathomable that another coronavirus outbreak could occur. The good news is that techniques in structural biology are advancing at light speed, and Dr. Crichlow says the RCSB PDB has adapted to accommodate the new techniques and the volume of entries.

The RCSB PDB and Nanome enhance access to the accumulating knowledge of the 3D structure and function of biological molecules in order to expand the frontiers of fundamental biology and medicine and enable scientists to meet the challenges of today and the future.

References

1. Young JY, Westbrook JD, Feng Z et al. (2018) Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data. Database

https://doi.org/10.1093/database/bay002

2. http://rcsb.org/covid19

3. Benton DJ, Wrobel AG, Xu P et al. (2020) Receptor binding and priming of the spike protein of SARS-CoV-2 for membrane fusion. Nature https://doi.org/10.1038/s41586-020-2772-0

4. Barnes CO, West AP Jr, Huey-Tubman KE et al. (2020) Structures of Human Antibodies Bound to SARS-CoV-2 Spike Reveal Common Epitopes and Recurrent Features of Antibodies. Cell https://doi.org/10.1016/j.cell.2020.06.025

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