Molecule of the Month: Fifty Years of Open Access to PDB Structures
The Protein Data Bank is celebrating its golden anniversary!
Structural Biology Begins
Elusive Membrane Channels
New Ways of Seeing Molecules
Exploring the Structure
Experimental and Predicted Structures of Myoglobin
As I write this article, the structural biology community is being transformed by the recent successes of AlphaFold2 and RoseTTAFold, which show a quantum leap in success rates for protein structure prediction. The example shown here is an easy one: the structure of human myoglobin predicted by AlphaFold2 (blue) is almost identical to the historic structure of whale myoglobin from Kendrew's laboratory (green, PDB ID 1mbn) and later structures of human myoglobin (click on the image for an interactive JSmol). Of course, there's only one reason that this structure is easy to predict: all predictive methods build on decades of structures available in the PDB archive. These predictive methods are a triumph of clever computing. They are also a triumph for the tens of thousands of researchers who have contributed to the PDB archive. The breadth of structural knowledge that is encompassed by their entries, and their willingness to make their structures freely available in the archive, made all this possible.
The same is true for the fields of drug discovery and development, vaccine development, enzyme engineering, bionanotechnology, and dozens more--all build on this goldmine of structural data to understand the basic principles of biomolecules, then apply them for new, breakthrough goals. Today, building on an explosion of new structure-determination techniques, the archive continues to grow rapidly. Who knows what will be possible? Exciting times are certainly ahead for the next 50 years of the PDB!
Topics for Further Discussion
- If you want to learn more about the history of the PDB, take a look at this Timeline of PDB History.
- Many publications and educational materials celebrating the PDB50 anniversary are available on the RCSB PDB website.
Related PDB-101 Resources
- Browse Biomolecules
- Browse PDB Data
- Browse Biomolecular Structural Biology
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- 7cgo: Tan, J., Zhang, X., Wang, X., Xu, C., Chang, S., Wu, H., Wang, T., Liang, H., Gao, H., Zhou, Y., Zhu, Y. (2021) Structural basis of assembly and torque transmission of the bacterial flagellar motor. Cell 184: 2665-2679.e19
- wwPDB consortium (2019) Protein Data Bank: the single global archive for 3D macromolecular structure data. Nucl Acids Res 47: D520-D528
- Goodsell, D.S., Burley, S.K., Berman, H.M. (2013) Revealing structural views of biology. Biopolymers 99: 817-824
- 4v4q: Schuwirth, B.S., Borovinskaya, M.A., Hau, C.W., Zhang, W., Vila-Sanjurjo, A., Holton, J.M., Cate, J.H. (2005) Structures of the bacterial ribosome at 3.5 A resolution. Science 310: 827-834
- 1rqv: Bocharov, E.V., Sobol, A.G., Pavlov, K.V., Korzhnev, D.M., Jaravine, V.A., Gudkov, A.T., Arseniev, A.S. (2004) From structure and dynamics of protein L7/L12 to molecular switching in ribosome. J Biol Chem 279: 17697-17706
- 2brd: Grigorieff, N., Ceska, T.A., Downing, K.H., Baldwin, J.M., Henderson, R. (1996) Electron-crystallographic refinement of the structure of bacteriorhodopsin. J Mol Biol 259: 393-421
- 2tbv: Hopper, P., Harrison, S.C., Sauer, R.T. (1984) Structure of tomato bushy stunt virus. V. Coat protein sequence determination and its structural implications. J Mol Biol 177: 701-713
- 6tna: Sussman, J.L., Holbrook, S.R., Warrant, R.W., Church, G.M., Kim, S.H.(1978) Crystal structure of yeast phenylalanine transfer RNA. I. Crystallographic refinement. J Mol Biol 123: 607-630
- 1aga: Arnott, S., Fulmer, A., Scott, W.E., Dea, I.C., Moorhouse, R., Rees, D.A. (1974) The agarose double helix and its function in agarose gel structure. J Mol Biol 90: 269-284
- Crystallography: Protein Data Bank. (1971) Nature New Biology 233: 223
- 2dhb: Bolton, W., Perutz, M.F. (1970) Three dimensional fourier synthesis of horse deoxyhaemoglobin at 2.8 Angstrom units resolution. Nature 228: 551-552
- 1mbn: Watson, H.C. (1969) The stereochemistry of the protein myoglobin. Prog Stereochem 4: 299
October 2021, David Goodsellhttp://doi.org/10.2210/rcsb_pdb/mom_2021_10