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(-) Introduction

by Jürgen Sühnel

In this compilation the very first biopolymer structures contained in the Protein Data Bank (PDB) are listed by molecule type, method of structure determination and deposition date. Except for a few examples, published structures NOT deposited at the PDB and obsolete PDB entries are NOT included. Note further, that in the early days of structural biology the PDB did not yet exist. It was created in 1970-1971.

The first three-dimensional structure of a biopolymer was the DNA model built by J. D. Watson and F. H. C. Crick in 1953 taking into account fiber diffraction data provided by M. H. F. Wilkins and others (Nobel Prize in Physiology or Medicine, 1962). Here is a copy of the original paper submitted to Nature on April 2, 1953 and published on April 25, 1953.

The first three-dimensional protein structures (myoglobin and hemoglobin) were determined by M. F. Perutz and J. C. Kendrew (Nobel Prize in Chemistry, 1962). The entries included in the PDB (PDB codes: 1mbn and 2dhb) represent refined structures. J. C. Kendrew had obtained a myoglobin structure at a resolution of 6 Å already in 1957.

A. Klug has contributed substantially to the development of electron microscopy. This method is suitable for systems that cannot be crystallized (Nobel Prize in Chemistry, 1982). A. Klug has applied this method primarily to virus structures (see for example, Finch, Klug, J. Mol. Biol. 1965, 13, 1-12).

The structure of the first membrane-bound protein (a photosynthetic reaction centre; PDB code: 1prc) was resolved by J. Deisenhofer, R. Huber and H. Michel (Nobel Prize in Chemistry, 1988).

The first three-dimensional protein structure determined by NMR spectroscopy (proteinase IIa inhibitor from bull seminal plasma (PDB codes: 1bus, 2bus) was reported by K. Wüthrich and co-workers in 1985 (Nobel Prize in Chemistry, 2002).

 First Structures Listed by Molecule Type and Deposition Date

(-) Proteins

PDB code structure method year of publication deposition date release date publication authors
1sbt subtilisin X-ray diffraction 1971 11-Aug-1972  06-Jan-1977 R. A. Alden, J. J. Birktoft, J. Kraut, J. D. Robertus, C. S. Wright 
1mbn myoglobin X-ray diffraction 1969 05-Apr-1973  19-May-1976 H. C. Watson (J. C. Kendrew)
2dhb hemoglobin X-ray diffraction 1970 01-Nov-1973  07-Jun-1977 W. Bolton, M. F. Perutz
3ldh lactate dehydrogenase X-ray diffraction 1976 06-Jun-1974 29-Apr-1977 J. L. White, M. L. Hackert, M. Buehner, M. J. Adams, G. C. Ford, P. J. Lentz Junior, I. E. Smiley, S. J. Steindel, M. G. Rossmann
1lyz lysozyme X-ray diffraction 1974 01-Feb-1975 12-Apr-1977 R. Diamond

As noted above, the first three-dimensional protein structures (myoglobin and hemoglobin) were determined by J. C. Kendrew and M. F. Perutz (Nobel Prize in Chemistry, 1962). The entries included in the PDB (PDB codes: 1mbn and 2dhb) represent refined structures. The obsolete hemoglobin entry 1dhb has the same deposition date as 2dhb. J. C. Kendrew had obtained a myoglobin structure at a resolution of 6 Å already in 1957. An early paper on the myoglobin structure paper was published in 1960 (Kendrew, J.C., Strandberg, B.E., Hart, R.G., Davies, D.R., Phillips, D.C., Shore, V.C. Nature 1960, 185:422-427). Subtilisin (1sbt) is the first enzyme currently included in the PDB and the related paper was published in 1971. An earlier subtilisin structure paper by the same authors was published in 1969. The first lysozyme structure included in the current PDB has the code 1lyz and the related paper was published in 1974. A much earlier lysozyme structure paper appeared in 1965. So, lysozyme was very likely the first enzyme structure.

Thanks to M.S. Weiss for information on a few early papers.

(-) Carbohydrates

PDB code structure method year of publication deposition date release date publication authors
1hya hyaluronic acid X-ray diffraction 1975 20-Nov-1977 28-Mar-1980 W. T. Winter, P. J. C. Smith, S. Arnott
2hya | 3hya hyaluronic acid X-ray diffraction 1975 20-Nov-1977 28-Mar-1980 J. M. Guss, D. W. L. Hukins, P. J. C. Smith, W. T. Winter, S. Arnott, R. Moorhouse, D. A. Rees
4hya hyaluronic acid X-ray diffraction 1977 20-Nov-1977 28-Mar-1980 W. T. Winter, S. Arnott

(-) RNA

PDB/NDB code structure method year of publication deposition date release date publication authors
4tna/trna10 yeast phenylalanine transfer RNA X-ray diffraction 1978 12-Apr-1978  17-May-1978 B. E. Hingerty, R. S. Brown, A. Jack 
6tna/trna04 yeast phenylalanine transfer RNA X-ray diffraction 1978 16-Nov-1978  16-Jan-1979 J. L. Sussman, S. R. Holbrook, R. W. Warrant, G. M. Church, S. -H. Kim 

Earlier reports on 4tna appeared in 1974 and 1975. The structure 6tna was earlier described in 1976 (I, II). Early descriptions of the obsolete entry 2tna superseded by 7tna, 8tna and 1tra were given in 1972 and 1976.

(-) DNA

PDB/NDB code structure method year of publication deposition date release date publication authors
1bna/bdl001 B-DNA dodecamer X-ray diffraction 1981 26-Jan-1981  21-May-1981 H. R. Drew, R. M. Wing, T. Takano, C. Broka, S. Tanaka, K. Itakura, R. E. Dickerson 
1zna/zdd015 Z-DNA tetramer X-ray diffraction 1981 26-Jan-1981  18-Mar-1981 H. R. Drew, R. E. Dickerson 
2zna | 3zna Z-DNA dodecamer theoretical model 1981 10-Feb-1981 21-May-1981 A. H. -J. Wang, G. J. Quigley, F. J. Kolpak, G. Van Der Marel, J. H. Van Boom, A. Rich
2bna/bdl002 B-DNA dodecamer X-ray diffraction 1982 12-Nov-1981 03-Feb-1982 H. R. Drew, S. Samson, R. E. Dickerson
3bna/bdlb03 | 4bna/bdlb04 B-DNA dodecamer X-ray diffraction 1982 16-Feb-1982 15-Apr-1982 A. V. Fratini, M. L. Kopka, H. R. Drew, R. E. Dickerson
1ana/addb01 A-DNA tetramer X-ray diffraction 1984 04-Jun-1982 29-Jul-1982 B. N. Conner, C. Yoon, J. L. Dickerson, R. E. Dickerson
1dnn DNA in chromatin theoretical model 1979 29-Nov-1982 09-Mar-1983 J. L. Sussman, E. N. Trifonov

The very first bioplymer structure paper describes the desoxyribose nucleic acid structure model generated by Watson and Crick (J. D. Watson, F.H. C. Crick, Nature 1953, 171, 737).

(-) DNA/Drug Complexes

PDB/NDB code structure method year of publication deposition date release date publication authors
5bna/ddl017 cis-platin/DNA complex X-ray diffraction 1984 22-Aug-1983 02-Nov-1983 R. M. Wing, P. Pjura, H. R. Drew, R. E. Dickerson
6bna/gdlb05 netropsin/DNA complex X-ray diffraction 1985 30-Aug-1984  29-Oct-1984 M. L. Kopka, C. Yoon, D. Goodsell, P. Pjura, R. E. Dickerson
8bna/gdl006 Hoechst 33258/ DNA complex X-ray diffraction 1987 29-Aug-1986 15-Jun-1987 P. E. Pjura, K. Grzeskowiak, R. E. Dickerson

(-) DNA/Protein Complexes

PDB/NDB code structure method year of publication deposition date release date publication authors
2gap catabolite gene activator protein-DNA complex theoretical model 1984 06-Mar-1986  07-May-1986 I. T. Weber, T. A. Steitz 
2dnj/pde006 dnase I-octamer complex X-ray diffraction 1991 21-Oct-1986 31-Jan-1994 A. Lahm, D. Suck
2or1/pdr004 phage 434 repressor complex with a synthetic DNA operator X-ray diffraction 1988 05-Sep-1989 15-Jul-1990 A. K. Aggarwal, D. W. Rodgers, M. Drottar, M. Ptashne, S. C. Harrison 
3cro/pdr001 phage 434 Cro/OR1 complex X-ray diffraction 1991 26-Jul-1990  15-Oct-1991 A. Mondragon, S. C. Harrison 

(-) RNA/Protein Complexes

- RNA/protein complexes

PDB/NDB code structure method year of publication deposition date release date publication authors
2tmv tobacco mosaic virus capsid (TMV) complexed RNA fiber diffraction 1989 15-Sep-1988 09-Jan-1989 K. Namba, R. Pattanayek, G. Stubbs
1bmv/prv001 bean-pod mottle virus (BPMV) capsid complexed with RNA X-ray diffraction 1989 09-Oct-1989  15-Jul-1990 Z. Chen, C. Stauffacher, Y. Li, T. Schmidt, W. Bomu, G. Kamer, M. Shanks, G. Lomonossoff, J. E. Johnson 
1gsg/ptr001 glutaminyl transfer RNA synthetase complexed with transfer RNA(Gln) and ATP X-ray diffraction 1989 03-Apr-1990 15-Jan-1992 M. A. Rould, J. J. Perona, D. Soell, T. A. Steitz

 First Structures Listed by Method of Structure Determination and Deposition Date

(-) X-ray

PDB/NDB code structure method year of publication deposition date release date publication authors
1sbt subtilisin X-ray diffraction 1971 11-Aug-1972  06-Jan-1977 R. A. Alden, J. J. Birktoft, J. Kraut, J. D. Robertus, C. S. Wright 
1mbn myoglobin X-ray diffraction 1969 05-Apr-1973  19-May-1976 H. C. Watson (J. C. Kendrew)
2dhb hemoglobin X-ray diffraction 1970 01-Nov-1973  07-Jun-1977 W. Bolton, M. F. Perutz

(-) Theoretical Models

PDB/NDB code structure method year of publication deposition date release date publication authors
1rlx | 2rlx | 3rlx | 4rlx relaxin model 1978 13-Mar-1978 23-May-1978 N. Isaacs, R. James, H. Niall, G. Bryant-Greenwood, G. Dodson, A. Evans, A. C. T. North
1mlp murein lipoprotein model 1978 28-Aug-1978 13-Oct-1978 A. D. Mc Lachlan 
1tnc troponin model 1975 !!! 15-Jul-1980  09-Aug-1980 R. H. Kretsinger, C. D. Barry
2zna | 3zna Z-DNA model 1981 10-Feb-1981 21-May-1981 A. H. -J. Wang, G. J. Quigley, F. J. Kolpak, G. Van Der Marel, J. H. Van Boom, A. Rich

(-) Fiber Diffraction

PDB/NDB code structure method year of publication deposition date release date publication authors
1aga agarose fiber diffraction 1974 23-May-1978 28-Mar-1980 S. Arnott, A. Fulmer, W. E. Scott, I. C. M. Dea, R. Moorhouse, D. A. Rees
1kes keratan sulfate fiber diffraction 1974 23-May-1978 28-Mar-1980 S. Arnott, J. M. Guss, D. W. L. Hukins, I. C. M. Dea, D. A. Rees 
2tmv tobacco mosaic virus  fiber diffraction 1989 15 Sep 1988  09-Jan-1989 K. Namba, R. Pattanayek, G. Stubbs 

(-) Neutron Diffraction or Joint Neutron/X-ray Diffraction

PDB/NDB code structure method year of publication deposition date  release date publication authors
5rsa ribonucelase A neutron/X-ray diffraction 1986 29-Apr-1985 17-Jul-1985 A. Wlodawer, N. Borkakoti, D. S. Moss, B. Howlin
6rsa ribonuclease A complex with uridine vanadate neutron/X-ray diffraction 1985 25-Feb-1986 07-May-1986 B. Borah, C. -W. Chen, W. Egan, M. Miller, A. Wlodawer, J. S. Cohen 
1ntp modified beta trypsin neutron diffraction 1984 16-Sep-1987 16-Jan-1988 A. A. Kossiakoff

(-) NMR

PDB/NDB code structure method year of publication deposition date  release date publication authors
1bds | 2bds antihypertensive and antiviral protein BDS NMR 1989 14-Nov-1988 09-Jan-1989 P. C. Driscoll, A. M. Gronenborn, L. Beress, G. M. Clore 
2hir | 4hir hirudin NMR 1989 19-Dec-1988 15-Jan-1990 P. J. M. Folkers, G. M. Clore, P. C. Driscoll, J. Dodt, S. Koehler, A. M. Gronenborn 
2ait tendamistat NMR 1988 24-May-1989 15-Apr-1990 A. D. Kline, W. Braun, K. Wuthrich 
2cbh C-terminal domain of cellobiohydrolase  NMR 1989 30-May-1989 15-Jan-1990 P. J. Kraulis, G. M. Clore, M. Nilges, T. A. Jones, G. Pettersson, J. Knowles, A. M. Gronenborn 
1bus | 2bus proteinsae inhibitor IIa from bull seminal plasma NMR 1985 14-May-1990 15-Apr-1991 P. Guntert, M. P. Williamson, T. F. Havel, K. Wuthrich

The first protein structure solved by NMR spectroscopy (proteinase inhibitor II from bull seminal plasma; PDB codes: 1bus, 2bus) was reported in 1985 (Williamson MP, Havel TF, Wuthrich K. J Mol Biol. 1985, 182, 295-315). This structure was, however, later deposited at the PDB than the other NMR structures mentioned above.

(-) Electron Diffraction/Electron Microscopy

PDB/NDB code structure method year of publication deposition date  release date publication authors
1brd bacteriorhodopsin electron diffraction 1990 23-May-1990 15-Apr-1991 R. Henderson, J. M. Baldwin, T. A. Ceska, F. Zemlin, E. Beckmann, K. H. Downing 
2rec reca hexamer electron microscopy 1997 03-Dec-1996 01-Apr-1997 X. Yu, E. H. Egelman
1at9 bacteriorhodopsin electron diffraction 1997 20-Aug-1997 16-Sep-1998 Y. Kimura, D. G. Vassylyev, A. Miyazawa, A. Kidera, M. Matsushima, K. Mitsuoka, K. Murata, T. Hirai, Y. Fujiyoshi 
1tub alpha beta tubulin dimer electron diffraction 1998 23-Sep-1997 07-Oct-1998 E. Nogales, S. G. Wolf, K. H. Downing 
1kvp spiroplasma virus electron microscopy 1998 12-Dec-1997 23-Feb-1999

P. R. Chipman, M. Agbandje-Mckenna, J. Renaudin, T. S. Baker, R. Mckenna