The very first three-dimensional biopolymer structures

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

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.