SUPPLEMENTARY TABLES & REFERENCES
Biocrystallography: past, present, future
Richard Giegé and Claude Sauter
Architecture et Réactivité de l’ARN, Université de Strasbourg, CNRS, IBMC, 15 rue René Descartes, 67084 Strasbourg, France
REVISED – 02/03/10
~13000 characters in revised version (instead 11600 in submitted manuscript)
Supplementary Table S1. Biocrystallography over 6 decades: from architectural motifs to molecular structures of increasing complexity
Year
Macromolecular system
1951
Milestones
Initial references
-helix & -sheet*
Model based on X-ray structures of amino acids and
stereochemistry
(Pauling and Corey, 1951)
1953
DNA double helix*
Model based on fiber diffraction and stereochemistry
(Watson and Crick,1953)
1958–60
myoglobin*
5.5–2.0
, 153 aa
Existence of -helices
(Kendrew et al., 1960)
1960–68
hemoglobin*
5.5–2.8
22, 141-146 aa
Existence of quaternary structures and -helices
(Perutz et al., 1968)
1962–65
lysozyme
6.0–2.0
, 129 aa
First enzyme visualizing -sheets in a protein structure; became
a key model in crystallogenesis studies
(Blake et al., 1965)
1973
RNA double helical fragment
0.8
dinucleotides
Visualizing RNA double helix at atomic resolution (based on
riboGpC and ApU structures)
(Day et al., 1973; Rosenberg et al., 1973)
1974
tRNAPhe
3.0
76 nts; ~27 kDa
Structure of a functional RNA
(Kim et al., 1974; Robertus et al., 1974;
Suddath et al., 1974)
1974
D-glyceraldehyde-3-phosphate
dehydrogenase
2.9
2, 73 kDa
Discovery of nucleotide binding fold (Rossmann fold with
 topology) in lobster enzyme
(Moras et al., 1975; Rossmann et al.,
1974)
1978
tomato bushy stunt virus (TBSV)
2.9

T =3 Spherical RNA virus
(Harrison et al., 1978)
1984
photosynthetic reaction center*
3.0
 + 9 ligands, 143 kDa
Membrane protein supramolecular assembly
(Deisenhofer et al., 1984)
1991
bacterial porin
1.8
32 kDa
Integral membrane protein with 16-stranded -barrel
(Weiss et al., 1991)
1992
leucine zipper protein motif
interacting with DNA
2.9
20 bp DNA; 58 aa peptide
A helix-turn-helix motif for DNA recognition found in many
regulatory proteins
(Ellenberger et al., 1992)
1993
zinc-fingers from the Tramtrack
protein interacting with DNA
2.8
19 bp DNA; 66 aa peptide
Examples of two Cys2–His2 zinc-fingers, a widely occurring
DNA-binding motif
(Fairall et al., 1993)
1993
TATA box region in complex with
transcription factor
2.25–2.5
8 bp DNA; ~200 aa protein
Transcription factor induced conformational change in DNA
promoter region
(Kim et al., 1993a; Kim et al., 1993b)
1994
F1-ATPase*
2.8
33; 354 kDa
Molecular motor for ATP synthesis in mitochondria
(Abrahams et al., 1994)
1994
hammerhead ribozyme
2.6
34 nts-long
Structure of a RNA enzyme in complex with a 13 nts-long DNA
inhibitor
(Pley et al., 1994; Scott et al., 1995)
1997
nucleosome core particle
2.8
histone octamer + 146 bp
DNA; 184 kDa
Basic unit of chromatin
(Luger et al., 1997)
1997
bacteriorhodopsin
2.5
 + retinal; 27 kDa
Improved structure after crystallization in lipidic cubic phase
(Pebay-Peyroula et al., 1997)
1998
bacterial potassium channel*
3.2
4, 125 aa
Integral membrane protein without C-terminal domain
(Doyle et al., 1998)
1999
bacterial and archaeal ribosome*
4.5–7.0
30S, 50S, 70S;
up to ~2–3 MDa
Visualizing various functional states of the ribosome during
protein synthesis, including with bound tRNA
(Ban et al., 1999; Cate et al., 1999;
Clemons et al., 1999; Tocilj et al., 1999)
2000
yeast RNA polymerase II*
3.0
10 subunits; 3500 aa
Core of the transcription complex
(Cramer et al., 2000; Kornberg, 2007)
-adrenergic G protein-coupled
receptor
2.5
 chimerawith ligands;
60 kDa
Human truncated transmenbrane protein with fused T4lysozyme needed for crystallization
(Rosenbaum et al., 2007)
* Nobel prize award
Resolution (Å)
Structural characteristics
, 180 x 122 kDa
Supplementary Table S2. Evolution of sample requirements and crystallization methods
Year
Sample requirement
(volume per assay / amount per project)
Crystallization method
Comments
Reference
1840–1940
large samples
B
a crystallization from crude or enriched protein preparations
(McPherson, 1991)
1934
content of a baker / >10 mg
B
first diffraction pattern of a protein crystal (pepsine)
(Bernal and Crowfoot, 1934)
1968–1984
10–50 l / >1 g
VD
b e.g. for tRNAPhe
(Dock et al., 1984)
1980–1988
20 l / ~1/0.4 g protein/RNA*
VD
b crystals of a protein/tRNA complex
(Ruff et al., 1988)
1988
1 ml / ~10 g
B
c establishment of a solubility / phase diagram of a small model protein
(Howard et al., 1988)
1998
188 l / 7 mg
microgravity D in agarose gel
b, c data collection up to 1.2Å resolution at room temperature
(Sauter et al., 2002)
1999
16 l / 5 mg*
VD
b crystal/solution phase diagram for crystal optimization of a large protein
(Sauter et al., 1999)
2005
2 l & 6 l / 4 mg & 50 mg
VD & CD
b, c screening & optimization of a protein crystal
(Biertumpfel et al., 2005)
2007
0.6 –2 l / 5 mg*
VD
b engineering and purification protocol of a protein prone to aggregation
(Bonnefond et al., 2007)
2009
0.15 l / <1 mg
microfluidic CD
b, c development of a microfluidic crystallization and X-ray analysis chip
(Dhouib et al., 2009)
*Design and perfection of preparation protocols for preparation of monodisperse protein samples suitable to solve structures required substantial additional amounts of
purified materials. B, for batch; CD for counter-diffusion; D, for dialysis; VD, for vapor diffusion crystallization. Experiments for a analytical biochemistry, b structural
biology, and/or c crystallogenesis investigations.
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