The Road to 100,000 Entries: The Early Structures

The Road to 100,000 Entries: The Early Structures

With this week's update, the PDB archive contains 99,775 entries and will soon pass the milestone of 100,000. In the weeks leading up to this event, wwPDB is looking back at other PDB milestones.

Scientists first began to decipher the 3D structure of proteins at the level of individual atoms using X-ray crystallography in the 1950s. These views of the structures of myoglobin (1,2), hemoglobin (3), lysozyme (4,5), and ribonuclease (6,7) provided unexpected insights into the regularities and similarities of proteins, and relationships between sequence, structure and function, and evolution. The enormous potential for scientific discovery and understanding was recognized early and rewarded with several Nobel prizes (8). These early structures also inspired a new field of scientific endeavor: molecular structural biology.

 

IMages from the wwPDB calendar highlights the first entries deposited to the PDB archive.

Beginning with just seven entries–carboxypeptidase, chymotrypsin, cytochrome, hemoglobin (lamprey), lactate dehydrogenase, subtilisin, and trypsin inhibitor (9-15)–the PDB archive was established in 1971 to provide both a home and an access point to these information-rich structures. It is a testament to the vision and foresight of the pioneers in the field that they understood the value and potential of archiving and sharing data in an era when computer networking was virtually non-existent.



Since its inception, the size of the archive has increased by a factor of 10 roughly every 10-15 years: the PDB reached 100 released entries in 1982, 1000 entries in 1993, and 10,000 in the year 2000. When the 100,000th is made available in May 2014, ~90% of the archive will have been released in the past fourteen years.

For a look at some of the milestone entries in the archive, see at RCSB PDB's Molecule of the Month; in Biophysical Journal, in Biopolymers; and in FEBS Journal.

PDB structures are also regularly highlighted in , , and the at RCSB PDB ().

 

  1. J. C. Kendrew, R. E. Dickerson, B. E. Strandberg, et al. (1960) Structure of myoglobin: A three-dimensional Fourier synthesis at 2 A. resolution. Nature 185: 422-427.
  2. J. C. Kendrew, G. Bodo, H. M. Dintzis, et al. (1958) A three-dimensional model of the myoglobin molecule obtained by x-ray analysis. Nature 181: 662-666.
  3. M. F. Perutz, M. G. Rossmann, A. F. Cullis, et al. (1960) Structure of haemoglobin: a three-dimensional Fourier synthesis at 5.5 Ã… resolution, obtained by X-ray analysis. Nature 185: 416-422.
  4. C. C. F. Blake, L. N. Johnson, G. A. Mair, et al. (1967) Crystallographic studies of the activity of hen egg-white lysozyme. Proc. R. Soc. London Ser. B 167: 378-388.
  5. C. C. F. Blake, D. F. Koenig, G. A. Mair, et al. (1965) Structure of hen egg-white lysozyme. A three dimensional Fourier synthesis at 2 Ã… resolution. Nature 206: 757-761.
  6. G. Kartha, J. Bello, D. Harker. (1967) Tertiary structure of ribonuclease. Nature 213: 862-865.
  7. H. W. Wyckoff, K. D. Hardman, N. M. Allewell, et al. (1967) The structure of ribonuclease-S at 6 Ã… resolution. J. Biol. Chem. 242: 3749-3753.
  8. M. Jaskolski, Z. Dauter, A. Wlodawer. (2014) A brief history of macromolecular crystallography, illustrated by a family tree and its Nobel fruits. FEBS Journal in press.
  9. D. W. Christianson, W. N. Lipscomb. (1986) X-ray crystallographic investigation of substrate binding to carboxypeptidase A at subzero temperature. Proc Natl Acad Sci U S A 83: 7568-7572.
  10. J. J. Birktoft, D. M. Blow. (1972) Structure of crystalline alpha-chymotrypsin. V. The atomic structure of tosyl-alpha-chymotrypsin at 2 Ã… resolution. J Mol Biol 68: 187-240.
  11. R. C. Durley, F. S. Mathews. (1996) Refinement and structural analysis of bovine cytochrome b5 at 1.5 A resolution. Acta Crystallogr D Biol Crystallogr 52: 65-76.
  12. W. A. Hendrickson, W. E. Love, J. Karle. (1973) Crystal structure analysis of sea lamprey hemoglobin at 2 Ã… resolution. J Mol Biol 74: 331-361.
  13. C. Abad-Zapatero, J. P. Griffith, J. L. Sussman, et al. (1987) Refined crystal structure of dogfish M4 apo-lactate dehydrogenase. J Mol Biol 198: 445-467.
  14. R. A. Alden, J. J. Birktoft, J. Kraut, et al. (1971) Atomic coordinates for subtilisin BPN' (or Novo). Biochem Biophys Res Commun 45: 337-344.
  15. M. Marquart, Walter, J., Deisenhofer, J., Bode, W., Huber, R. (1983) The geometry of the reactive site and of the peptide groups in trypsin, trypsinogen and its complexes with inhibitors. Acta Crystallogr B39: 480.