International
Tables for
Crystallography
Volume G
Definition and exchange of crystallographic data
Edited by S. R. Hall and B. McMahon

© International Union of Crystallography 2006
International Tables for Crystallography (2006). Vol. G. ch. 3.6, pp. 181-182

Section 3.6.7.5.2. Secondary structure

P. M. D. Fitzgerald,a* J. D. Westbrook,b P. E. Bourne,c B. McMahon,d K. D. Watenpaughe and H. M. Bermanf

a Merck Research Laboratories, Rahway, New Jersey, USA,bProtein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, Department of Chemistry and Chemical Biology, 610 Taylor Road, Piscataway, New Jersey, USA,cResearch Collaboratory for Structural Bioinformatics, San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0537, USA,dInternational Union of Crystallography, 5 Abbey Square, Chester CH1 2HU, England,eretired; formerly Structural, Analytical and Medicinal Chemistry, Pharmacia Corporation, Kalamazoo, Michigan, USA, and fProtein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, Department of Chemistry and Chemical Biology, 610 Taylor Road, Piscataway, New Jersey, USA
Correspondence e-mail:  paula_fitzgerald@merck.com

3.6.7.5.2. Secondary structure

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The data items in these categories are as follows:

(a) STRUCT_CONF_TYPE [Scheme scheme147]

(b) STRUCT_CONF [Scheme scheme148]

The bullet ([\bullet]) indicates a category key. The arrow ([\rightarrow]) is a reference to a parent data item.

The primary structure of a macromolecule is defined by the sequence of the components (amino acids, nucleic acids or sugars) in the polymer chain. The polymer chains assume conformations based on the torsion angles adopted by the rotatable bonds in the polymer backbone; the resulting conformations are referred to as the secondary structure of the polymer. Several patterns of values of backbone torsion angles have been described and given names, such as α-helix, β-strand, turn and coil for proteins, and A-, B- and Z-helix for nucleic acids.

In the mmCIF dictionary, these secondary structures are described in the STRUCT_CONF and STRUCT_CONF_TYPE categories. Note that the data items in these categories describe only the secondary structure; the tertiary organization of β-strands into β-sheets is described in the STRUCT_SHEET_* categories. There are no data items for describing the tertiary organization of α-helices or nucleic acids in the current version of the mmCIF dictionary.

The relationships between categories used to describe secondary structure are shown in Fig. 3.6.7.9[link].

[Figure 3.6.7.9]

Figure 3.6.7.9 | top | pdf |

The family of categories used to describe secondary structure. Boxes surround categories of related data items. Data items that serve as category keys are preceded by a bullet ([\bullet]). Lines show relationships between linked data items in different categories with arrows pointing at the parent data items.

The type of the secondary structure is specified in the STRUCT_CONF_TYPE category, along with the criteria used to identify it. The range of monomers assigned to each secondary-structure element is given in the STRUCT_CONF category.

The allowed values for the data item _struct_conf_type.id cover most types of protein and nucleic acid secondary structure (Example 3.6.7.9[link]). The criteria that define the secondary structure may be given using the data item _struct_conf_type.criteria. _struct_conf_type.reference can be used to specify a reference to the literature in which the criteria are explained in more detail.

Example 3.6.7.9. Secondary structure in an HIV-1 protease structure (PDB 5HVP) described with data items in the STRUCT_CONF_TYPE and STRUCT_CONF categories.

[Scheme scheme149]

The residues that define the beginning and end of each region of secondary structure are identified with the appropriate *_asym, *_comp and *_seq identifiers. The standard labelling system or the author's alternative labelling system may be used. The identification of the residues assigned to each region of secondary structure is linked to the labelling information in the ATOM_SITE category. Unusual features of a conformation may be described using _struct_conf.details.








































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