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

International Tables for Crystallography (2006). Vol. G, ch. 3.6, pp. 179-181

Section 3.6.7.5.1. Higher-level macromolecular structure

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

aMerck 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

3.6.7.5.1. Higher-level macromolecular structure

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The data items in these categories are as follows:

(a) STRUCT [Scheme scheme139]

(b) STRUCT_ASYM [Scheme scheme140]

(c) STRUCT_BIOL [Scheme scheme141]

(d) STRUCT_BIOL_GEN [Scheme scheme142]

(e) STRUCT_BIOL_KEYWORDS [Scheme scheme143]

(f) STRUCT_BIOL_VIEW [Scheme scheme144]

(g) STRUCT_KEYWORDS [Scheme scheme145]

The bullet ([\bullet]) indicates a category key. Where multiple items within a category are marked with a bullet, they must be taken together to form a compound key. The arrow ([\rightarrow]) is a reference to a parent data item.

The data items in these categories serve two related but distinct purposes.

The first purpose is to label each of the entities in the asymmetric unit, using data items in the STRUCT_ASYM category. These labels become part of the category key that identifies each coordinate record and they are used extensively throughout the STRUCT family of categories, so care must be taken to select a labelling scheme that is concise and informative.

The second function is descriptive. The categories descending from STRUCT_BIOL allow the author of the mmCIF to identify and annotate the biologically relevant structural units found by the structure determination. What constitutes a biological unit can depend on the context. Take the case of a structure with two polymers related by noncrystallographic symmetry, each of which binds a small-molecule cofactor. If the author wishes to describe the dimer interface, the biological unit could be taken to be the two protein molecules. If the author wishes to highlight the cofactor binding mode, the biological unit could be taken to be one protein molecule and its bound cofactor. In this second case, there could be an additional biological unit of the second protein molecule and its bound cofactor, which may or may not be identical in conformation to the first.

The relationships between categories used to describe higher-level structure are illustrated in Fig. 3.6.7.7[link].

[Figure 3.6.7.7]

Figure 3.6.7.7 | top | pdf |

The family of categories used to describe the higher-level macromolecular 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 STRUCT category serves to link the structure to the overall identifier for the data block, using _struct.entry_id, and to supply a title that describes the entire structure. The importance of this title as a succinct description of the structure should not be underestimated, and the author should express concisely but clearly in _struct.title the components of interest and the importance of this particular study. It is useful to think of this title as describing the motivation for the structure determination, rather than the result. For instance, if the goal of the study was to determine the structure of enzyme A at pH 7.2 as part of a study of the mechanism of the reaction catalysed by the enzyme, an appropriate value for _struct.title would be `Enzyme A at pH 7.2', even if the structure was found to contain two molecules per asymmetric unit, a bound calcium ion and a disordered loop between residues 47 and 52.

The STRUCT_KEYWORDS category allows an author to include keywords for the structure that has been determined. Other categories, such as STRUCT_BIOL_KEYWORDS and STRUCT_SITE_KEYWORDS, allow more specific keywords to be given, but the STRUCT_KEYWORDS category is the most likely category to be searched by simple information retrieval applications, so the author of an mmCIF might want to duplicate any keywords given elsewhere in the mmCIF in STRUCT_KEYWORDS as well.

The chemical entities that form the contents of the asymmetric unit are identified using data items in the ENTITY categories. The data items in the STRUCT_ASYM category link these entities to the structure itself. A unique identifier is attached to each occurrence of each entity in the asymmetric unit using _struct_asym.id. This identifier forms a part of the atom label in the ATOM_SITE category, which is used throughout the many categories in the STRUCT group in describing the structure. The identifier is also used in generating biological assemblies.

The usual reason for determining the structure of a biological macromolecule is to get information about the biologically relevant assemblies of the entities in the crystal structure. These assemblies take many forms and could encompass the complete contents of the asymmetric unit, a fraction of the contents of the asymmetric unit or the contents of more than one asymmetric unit. Each assembly, or `biological unit', is given an identifier in the STRUCT_BIOL category and the author may annotate each biological unit using the data item _struct_biol.details. Keywords for each biological unit can be given using data items in the STRUCT_BIOL_KEYWORD category.

The entities that comprise the biological unit are specified using data items in the STRUCT_BIOL_GEN category by reference to the appropriate values of _struct_asym.id and by specifying any symmetry transformation that must be applied to the entities to generate the biological unit.

Data items in the STRUCT_BIOL_VIEW category allow the author to specify an orientation of the biological unit that provides a useful view of the structure. The comments given in _struct_biol_view.details may be used as a figure caption if the view is intended to be a figure in a report describing the structure.

The example of crambin in Section 3.6.3[link] shows the relations between the categories defining higher-level structure for the straightforward case of a single protein molecule (with a small co-crystallization molecule and solvent) in the asymmetric unit. The structure of HIV-1 protease with a bound inhibitor (PDB 5HVP), shown in Example 3.6.7.8[link], is considerably more complex. There are two entities: the monomeric form of the enzyme and the small-molecule inhibitor. The asymmetric unit contains two copies of the enzyme monomer (both fully occupied) and two copies of the inhibitor (each of which is partially occupied) (Fig. 3.6.7.8[link]). Three biological assemblies are constructed for this system. One biological unit contains only the dimeric enzyme (Fig. 3.6.7.8[link]b), the second contains the dimeric enzyme with one partially occupied conformation of the inhibitor (Fig. 3.6.7.8[link]c) and the third contains the dimeric enzyme with the second partially occupied conformation of the inhibitor (Fig. 3.6.7.8[link]d). There are alternative conformations of the side chains in the enzyme that correlate with the binding mode of the inhibitor.

[Figure 3.6.7.8]

Figure 3.6.7.8 | top | pdf |

The higher-level structure of the complex of HIV-1 protease with an inhibitor (PDB 5HVP) to be described with data items in the STRUCT_ASYM, STRUCT_BIOL, STRUCT_BIOL_KEYWORDS and STRUCT_BIOL_GEN categories. (a) Complete structure; (b), (c), (d) three different biological units.

Example 3.6.7.8. The higher-level structure of the complex of HIV-1 protease with an inhibitor (PDB 5HVP) described with data items in the STRUCT_ASYM, STRUCT_BIOL, STRUCT_BIOL_KEYWORDS and STRUCT_BIOL_GEN categories.

[Scheme scheme146]








































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