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. 145-147

Section 3.6.3. Overview of the mmCIF data model

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

3.6.3. Overview of the mmCIF data model

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The solution and refinement of a macromolecular structure is complex and often difficult, as there are a large number of atoms in a typical macromolecule, the molecular conformation can be complex and it can be difficult to model included solvent molecules. However, even when a satisfactory structural model has been derived, describing the structure can be a considerable challenge. Using diagrams can help, but two-dimensional projections are often inadequate for illustrating important features and a complete understanding of the three-dimensional structure of a macromolecule can often only be reached by using interactive molecular graphics software.

The mmCIF dictionary provides several ways for describing the structure. The PUBL categories can be used to record text describing the structure. The complete list of atomic coordinates may be used as input for visualization programs that allow a range of wire-frame, stick, space-filling, ribbon or cartoon representations to be generated based upon inbuilt heuristics and user interaction. However, most importantly, the mmCIF approach also offers a large collection of categories which are designed to provide descriptions of the structure at different levels of detail, and the relationships between data items in different categories permit the function of an individual atom site at any particular level of detail to be traced.

Before beginning the detailed description of the full mmCIF dictionary, it is helpful to demonstrate how it is used to describe the structure of a biological macromolecule. Fig. 3.6.3.1[link] shows the small protein crambin, which is a single polypeptide chain of 48 residues. The molecule co-crystallizes with a molecule of ethanol, although this is not thought to have any biological effect. Almost a quarter of the residues have side chains that adopt alternative conformations, and there is sequence heterogeneity at positions 22 (Pro/Ser) and 25 (Leu/Ile). Three disulfide links stabilize the structure.

[Figure 3.6.3.1]

Figure 3.6.3.1 | top | pdf |

A representation of crambin (PDB 3CNR) with a co-crystallized ethanol molecule.

The highest level of the description of the structure uses data items from the STRUCT category group. The crystallographic asymmetric unit contains one protein molecule, one co-crystallization ethanol molecule and a water solvent molecule. These are described with data items from the STRUCT_ASYM category (Example 3.6.3.1[link]).

Example 3.6.3.1. Specification of the three distinct components of the crambin structure.

[Scheme scheme1]

Each entry in this list assigns a label to a discrete component of the asymmetric unit and associates it with an entry in the entity list that defines each distinct chemical species in the crystal (Example 3.6.3.2[link]).

Example 3.6.3.2. Specification of the distinct chemical entities in the crambin structure.

[Scheme scheme2]

The biological functions of the components of the crystal structure are described using data items in the STRUCT_BIOL and related categories. For crambin, the biological function is still unknown (see Example 3.6.3.3[link]). This example also shows how the biological unit is generated from specific discrete objects in the asymmetric unit. In this case the relationship is trivial, but it will often be much more complex.

Example 3.6.3.3. Identification of the biological function of the components of the crambin structure.

[Scheme scheme3]

The secondary structure of the protein is described using data items in the STRUCT_CONF category (and in the STRUCT_SHEET category where relevant). The beginning and end labels for each α-helix, β-strand or turn in Example 3.6.3.4[link] refer to the chemical components of the structural unit labelled chain_a at the given locations in the sequence (e.g. helix H1 runs from the isoleucine at position number 7 to the proline at position number 19 in the amino-acid sequence).

Example 3.6.3.4. Description of the secondary structure of crambin.

[Scheme scheme4]

Interactions between different parts of the structure are described using data items in the STRUCT_CONN and related categories. In Example 3.6.3.5[link], some of the disulfide bridges and intramolecular hydrogen bonds are reported. As with the secondary structural elements, the partners in the links are identified by complex labels that include the chemical component involved, the object within the asymmetric unit that is under consideration, the position in the amino-acid (or nucleotide) sequence and the individual atom.

Example 3.6.3.5. Interactions between parts of the crambin structure.

[Scheme scheme5]

The objects identified at the highest level of the description of the structure are arbitrary. To discover their chemical identity, one needs to consult the ENTITY category group. As indicated above, each separate chemical species in the crystal should be specified in the entity table. Chemical entities are classified as polymer, non-polymer or water. Non-polymeric molecules, such as the co-crystallized ethanol in this example, are described as distinct chemical components using data items in the CHEM_COMP family of categories. Polymeric molecules are described using data items in the ENTITY_POLY family of categories.

In Example 3.6.3.6[link], the natural source for crambin is described, the overall features of the polypeptide chain are listed and the component parts (in effect the amino-acid sequence) are tabulated. Note that sequence heterogeneity is described by allowing a sequence number to be correlated with more than one monomer identifier (in the example, sequence number 22 is assigned both to proline and serine, while 25 is assigned to both leucine and isoleucine). Sequence heterogeneity can be defined by assigning suitable labels in the ATOM_SITE list.

Example 3.6.3.6. Description of the crambin polypeptide.

[Scheme scheme6]

The individual amino acids in the protein sequence of Example 3.6.3.6[link] are labelled by the data item _entity_poly_seq.mon_id; this refers to the separate chemical components listed in the CHEM_COMP family of categories (Example 3.6.3.7[link]). As mentioned above, entries in these categories may be individual monomeric species within the crystal structure, or they may be amino acids or nucleotide bases that form the macromolecular polymer. In most cases, the entries recorded in these categories will be summaries of chemical information for standard amino acids and nucleotides, or references to external libraries of standard data for these. However, the categories contain enough data items to describe modified residues or co-crystallization factors in full if necessary.

Example 3.6.3.7. Separate chemical components forming the crambin polypeptide.

[Scheme scheme7]

At the most detailed level, the individual atom sites are described with data items in the ATOM category group, as shown for crambin in Example 3.6.3.8[link]. A few points about this example should be noted. The composite labelling of each site includes a pointer to the description of the parent molecule as a specific object in the asymmetric unit ( _atom_site.label_asym_id) and to the relevant monomeric building block of which the atom is a member ( _atom_site.label_comp_id). The label component _atom_site.label_alt_id indicates alternative conformations in which an atom site may be found. For example, the atom sites numbered 3 and 4 are alternative locations for the α-carbon of the terminal residue. It may be deduced from the occupancies that the alternative conformations A and B are modelled with 80% and 20%occupancy, respectively, but this can be stated explicitly using the ATOM_SITES_ALT category. The sequence heterogeneity at residue 22 is shown by the presence of pointers to proline and serine, and the occupancy factors show that proline and serine are present in the ratio 60 to 40. There is also an alternative conformation within the serine at residue 22, split equally across two sites.

Example 3.6.3.8. Partial listing of the atomic coordinates of crambin.

[Scheme scheme8]








































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