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3D complex: a structural classification of protein complexes.

Levy ED, Pereira-Leal JB, Chothia C, Teichmann SA - PLoS Comput. Biol. (2006)

Bottom Line: We also analyse the structures in terms of the topological arrangement of their subunits and find that they form a small number of arrangements compared with all theoretically possible ones.This is because most complexes contain four subunits or less, and the large majority are homomeric.In addition, there is a strong tendency for symmetry in complexes, even for heteromeric complexes.

View Article: PubMed Central - PubMed

Affiliation: Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom. elevy@mrc-lmb.cam.ac.uk

ABSTRACT
Most of the proteins in a cell assemble into complexes to carry out their function. It is therefore crucial to understand the physicochemical properties as well as the evolution of interactions between proteins. The Protein Data Bank represents an important source of information for such studies, because more than half of the structures are homo- or heteromeric protein complexes. Here we propose the first hierarchical classification of whole protein complexes of known 3-D structure, based on representing their fundamental structural features as a graph. This classification provides the first overview of all the complexes in the Protein Data Bank and allows nonredundant sets to be derived at different levels of detail. This reveals that between one-half and two-thirds of known structures are multimeric, depending on the level of redundancy accepted. We also analyse the structures in terms of the topological arrangement of their subunits and find that they form a small number of arrangements compared with all theoretically possible ones. This is because most complexes contain four subunits or less, and the large majority are homomeric. In addition, there is a strong tendency for symmetry in complexes, even for heteromeric complexes. Finally, through comparison of Biological Units in the Protein Data Bank with the Protein Quaternary Structure database, we identified many possible errors in quaternary structure assignments. Our classification, available as a database and Web server at http://www.3Dcomplex.org, will be a starting point for future work aimed at understanding the structure and evolution of protein complexes.

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Cyclic and Dihedral Symmetries(C2) Cyclic symmetry: two subunits are related by a single 2-fold axis, shown by a dashed line. An ellipse at the end of the symmetry axis marks a 2-fold axis. Nearly all homodimers have C2 symmetry. C2 symmetry is termed “2” in the crystallographic Hermann-Mauguin nomenclature, shown in red beneath C2.(C4) Cyclic symmetry: four subunits are related by one 4-fold axis. A square at the end of the symmetry axis marks a 4-fold axis.(D2) Dihedral symmetry: four subunits are related by three 2-fold axes. D2 symmetry can be constructed from two C2 dimers. Note the difference between the D2 and C4 symmetries: two symmetry types that both have four subunits.(D4) Dihedral symmetry: eight subunits are related to each other by one 4-fold axis and two 2-fold axes. Note that D4 symmetry can be constructed by stacking two C4 tetramers as shown, or four C2 dimers (not shown).
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pcbi-0020155-g006: Cyclic and Dihedral Symmetries(C2) Cyclic symmetry: two subunits are related by a single 2-fold axis, shown by a dashed line. An ellipse at the end of the symmetry axis marks a 2-fold axis. Nearly all homodimers have C2 symmetry. C2 symmetry is termed “2” in the crystallographic Hermann-Mauguin nomenclature, shown in red beneath C2.(C4) Cyclic symmetry: four subunits are related by one 4-fold axis. A square at the end of the symmetry axis marks a 4-fold axis.(D2) Dihedral symmetry: four subunits are related by three 2-fold axes. D2 symmetry can be constructed from two C2 dimers. Note the difference between the D2 and C4 symmetries: two symmetry types that both have four subunits.(D4) Dihedral symmetry: eight subunits are related to each other by one 4-fold axis and two 2-fold axes. Note that D4 symmetry can be constructed by stacking two C4 tetramers as shown, or four C2 dimers (not shown).

Mentions: Knowing the symmetry of a complex confers information about the 3-D arrangement of the subunits that is not provided by the graph representation. For example, there are two symmetric ways to arrange the subunits of a homotetramer. One is with a cyclic symmetry, in which the four subunits are related by a single 4-fold axis, called C4 symmetry, as shown in Figure 6. The other is a dihedral symmetry in which the four subunits are related by three 2-fold axes, called D2 symmetry (Figure 6). A priori, one cannot distinguish the two symmetry types from the graph representation alone. To assess whether the graph representation suffices to account for the spatial arrangement of the subunits, we asked whether QSs might contain complexes with different symmetries.


3D complex: a structural classification of protein complexes.

Levy ED, Pereira-Leal JB, Chothia C, Teichmann SA - PLoS Comput. Biol. (2006)

Cyclic and Dihedral Symmetries(C2) Cyclic symmetry: two subunits are related by a single 2-fold axis, shown by a dashed line. An ellipse at the end of the symmetry axis marks a 2-fold axis. Nearly all homodimers have C2 symmetry. C2 symmetry is termed “2” in the crystallographic Hermann-Mauguin nomenclature, shown in red beneath C2.(C4) Cyclic symmetry: four subunits are related by one 4-fold axis. A square at the end of the symmetry axis marks a 4-fold axis.(D2) Dihedral symmetry: four subunits are related by three 2-fold axes. D2 symmetry can be constructed from two C2 dimers. Note the difference between the D2 and C4 symmetries: two symmetry types that both have four subunits.(D4) Dihedral symmetry: eight subunits are related to each other by one 4-fold axis and two 2-fold axes. Note that D4 symmetry can be constructed by stacking two C4 tetramers as shown, or four C2 dimers (not shown).
© Copyright Policy
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC1636673&req=5

pcbi-0020155-g006: Cyclic and Dihedral Symmetries(C2) Cyclic symmetry: two subunits are related by a single 2-fold axis, shown by a dashed line. An ellipse at the end of the symmetry axis marks a 2-fold axis. Nearly all homodimers have C2 symmetry. C2 symmetry is termed “2” in the crystallographic Hermann-Mauguin nomenclature, shown in red beneath C2.(C4) Cyclic symmetry: four subunits are related by one 4-fold axis. A square at the end of the symmetry axis marks a 4-fold axis.(D2) Dihedral symmetry: four subunits are related by three 2-fold axes. D2 symmetry can be constructed from two C2 dimers. Note the difference between the D2 and C4 symmetries: two symmetry types that both have four subunits.(D4) Dihedral symmetry: eight subunits are related to each other by one 4-fold axis and two 2-fold axes. Note that D4 symmetry can be constructed by stacking two C4 tetramers as shown, or four C2 dimers (not shown).
Mentions: Knowing the symmetry of a complex confers information about the 3-D arrangement of the subunits that is not provided by the graph representation. For example, there are two symmetric ways to arrange the subunits of a homotetramer. One is with a cyclic symmetry, in which the four subunits are related by a single 4-fold axis, called C4 symmetry, as shown in Figure 6. The other is a dihedral symmetry in which the four subunits are related by three 2-fold axes, called D2 symmetry (Figure 6). A priori, one cannot distinguish the two symmetry types from the graph representation alone. To assess whether the graph representation suffices to account for the spatial arrangement of the subunits, we asked whether QSs might contain complexes with different symmetries.

Bottom Line: We also analyse the structures in terms of the topological arrangement of their subunits and find that they form a small number of arrangements compared with all theoretically possible ones.This is because most complexes contain four subunits or less, and the large majority are homomeric.In addition, there is a strong tendency for symmetry in complexes, even for heteromeric complexes.

View Article: PubMed Central - PubMed

Affiliation: Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom. elevy@mrc-lmb.cam.ac.uk

ABSTRACT
Most of the proteins in a cell assemble into complexes to carry out their function. It is therefore crucial to understand the physicochemical properties as well as the evolution of interactions between proteins. The Protein Data Bank represents an important source of information for such studies, because more than half of the structures are homo- or heteromeric protein complexes. Here we propose the first hierarchical classification of whole protein complexes of known 3-D structure, based on representing their fundamental structural features as a graph. This classification provides the first overview of all the complexes in the Protein Data Bank and allows nonredundant sets to be derived at different levels of detail. This reveals that between one-half and two-thirds of known structures are multimeric, depending on the level of redundancy accepted. We also analyse the structures in terms of the topological arrangement of their subunits and find that they form a small number of arrangements compared with all theoretically possible ones. This is because most complexes contain four subunits or less, and the large majority are homomeric. In addition, there is a strong tendency for symmetry in complexes, even for heteromeric complexes. Finally, through comparison of Biological Units in the Protein Data Bank with the Protein Quaternary Structure database, we identified many possible errors in quaternary structure assignments. Our classification, available as a database and Web server at http://www.3Dcomplex.org, will be a starting point for future work aimed at understanding the structure and evolution of protein complexes.

Show MeSH
Related in: MedlinePlus