Classification of macromolecules

Baker, T. S.; Henderson, R.

doi:10.1107/97809553602060000703

International
Tables for
Crystallography
Volume F
Crystallography of biological macromolecules
Edited by M. G. Rossmann and E. Arnold

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International Tables for Crystallography (2006). Vol. F. ch. 19.6, pp. 454-455 | 1 | 2 |

Section 19.6.4.2. Classification of macromolecules

T. S. Baker^a ^* and R. Henderson^b

^a Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907-1392, USA, and ^bMedical Research Council, Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, England
Correspondence e-mail: tsb@bragg.bio.purdue.edu

19.6.4.2. Classification of macromolecules

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The symmetry of a macromolecule or supramolecular complex is the primary determinant of how specimen preparation, microscopy, and 3D image reconstruction are performed (Sections 19.6.4.4 –19.6.4.6). The classification of molecules according to their level of periodic order and symmetry (Table 19.6.4.1) provides a logical and convenient way to consider the means by which specimens are studied in 3D by microscopy.

Table 19.6.4.1| top | pdf |
Classification of macromolecules according to periodic order and symmetry

Periodic order	Type	Symmetry	Example macromolecule/complex	Representative reference
0D	Point group	$[C_{1}]$	Ribosome	Frank (1997)
		$[C_{1}]$	Centriole	Kenney et al. (1997)
		$[C_{5}]$	Bacteriophage φ29 head	Tao et al. (1998)
		$[C_{8}]$	Ribonucleoprotein vault	Kong et al. (1999)
		$[C_{17}]$	TMV disc	Bloomer et al. (1978)
		$[D_{2}]$	β-Galactosidase	Jacobson et al. (1994)
		$[D_{6}]$	Clathrin coats	Vigers et al. (1986)
		$[D_{6}]$	Lumbricus terrestris haemoglobin	de Haas et al. (1997)
		T	Dps protein	Grant et al. (1998)
		O	Azotobacter pyruvate dehydrogenase core	Mattevi et al. (1992)
		I	Icosahedral viruses	Baker et al. (1999)
1D	Screw axis (helical) ^†		Acto-myosin filament	Milligan (1996)
			Acetylcholine receptor tubes	Miyazawa et al. (1999)
			Microtubule	Hirose et al. (1997)
			Bacterial flagella	Namba & Vonderviszt (1997)
			Tobacco mosaic virus	Jeng et al. (1989)
2D	2D space group (2D crystal)	p3	Bacteriorhodopsin membrane	Henderson et al. (1990)
		p42₁2	Aquaporin membrane	Cheng et al. (1997)
		p6	Gap junction membrane	Unger et al. (1999)
		p321	Light-harvesting complex II	Kühlbrandt et al. (1994)
		p12₁	Tubulin sheet	Nogales et al. (1998)
3D	3D space group (3D crystal)	$[P2_{1}2_{1}2_{1}]$	Myosin S1 protein crystal	Winkelmann et al. (1991)
3D	3D space group (3D crystal)	$[P6_{5}\hbox{ or }P6_{4}]$	Insect flight muscle	Taylor et al. (1997)

^†The symmetry of a helical structure is defined by an $[n_{m}]$ screw axis, which combines a rotation of 2π/n radians about an axis followed by a translation of m/n of the repeat distance. Because many helical structures are polymorphic, a different $[n_{m}]$ symmetry is needed to specify each polymorph. This designation can also be confusing: for example, for tobacco mosaic virus $[n_{m} = 16.333_{0.333}]$ , because the helical translational repeat consists of 49 subunits in three turns of the basic helix.

Each type of specimen offers a unique set of challenges in obtaining 3D structural information at the highest possible resolution. The best resolutions achieved by 3D EM methods to date, at about 3–4 Å, have been obtained with several thin 2D crystals (Henderson et al., 1990; Kühlbrandt et al., 1994; Nogales et al., 1998). These milestones have been achieved, in part, as a consequence of the excellent crystalline order exhibited by these specimens, but they are also attributable to dedicated efforts aimed at developing and refining a series of quantitative imaging and image-processing protocols, many of which are rooted in the principles and practice of Fourier-based methods used in X-ray crystallography.

With the exception of true 3D crystals, which must be sectioned to render them amenable (i.e. thin enough) to study by transmission electron microscopy, the resolutions obtained with biological specimens are generally dictated by the preservation of periodic order, and the symmetry and complexity of the object. Hence, studies of the helical acetylcholine receptor tubes (Miyazawa et al., 1999), the icosahedral hepatitis B virus capsid (Böttcher, Wynne & Crowther, 1997), the 70S ribosome (Gabashvili et al., 2000) and the centriole (Kenney et al., 1997) have yielded 3D density maps at resolutions of 4.6, 7.4, 11.5 and 280 Å, respectively.

If high resolution were the sole objective of EM, it would be necessary, given the capabilities of existing technology, to try to form well ordered 2D crystals or helical assemblies of each macromolecule of interest. Indeed, a number of different crystallization techniques have been devised (e.g. Horne & Pasquali-Ronchetti, 1974; Yoshimura et al., 1990; Kornberg & Darst, 1991; Jap et al., 1992; Kubalek et al., 1994; Rigaud et al., 1997; Hasler et al., 1998; Reviakine et al., 1998; Wilson-Kubalek et al., 1998) and some of these have yielded new structural information about otherwise recalcitrant molecules like RNA polymerase (Polyakov et al., 1998). However, despite the obvious technological advantages of having a molecule present in a highly ordered form, most macromolecules function not as highly ordered crystals or helices but instead as single particles (e.g. many enzymes) or, more likely, in concert with other macromolecules as occurs in supramolecular assemblies. Also, crystallization tends to constrain the number of conformational states a molecule can adopt and the crystal conformation might not be functionally relevant. Hence, though resolution may be restricted to much below that realized in the bulk of current X-ray crystallographic studies, cryo EM methods provide a powerful means to study molecules that resist crystallization in 1D, 2D or 3D. These methods allow one to explore the dynamic events, different conformational states (as induced, for example, by altering the microenvironment of the specimen) and macromolecular interactions that are the key to understanding how each macromolecule functions.

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International Tables for Crystallography (2006). Vol. F. ch. 19.6, pp. 454-455