3D Complex: A Structural Classification of Protein Complexes

By Emmanuel D. Levy, José B. Pereira-Leal, Cyrus Chothia, Sarah A. Teichmann. PLoS Comput. Biol., 2006

354 citations recorded by the source corpus.

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.

Subfields: Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/9379754e67cae2704e846bbd31918f920e50e812

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Citations in the corpus

Protein–protein interaction and quaternary structure (2008, methodology): “The results of the search are accessible through the PiQSi (Protein Quaternary Structure Investigation ; Lévy, 2007) database, which is derived from the 3D Complex database (Lévy et al. 2006), and interlinked with it.”
PDBe-KB: collaboratively defining the biological context of structural data (2021, background): “Barton Binding site predictions GBR 3D Complex (20) E.”
Principles of assembly reveal a periodic table of protein complexes (2015, methodology): “Alternatively, a graph representation, whichwe introduced several years ago, can be used to capture the main features of quaternary structure topology (9).”
The RCSB Protein Data Bank: views of structural biology for basic and applied research and education (2014, methodology): “To systematically characterize symmetry, pseudosymmetry and protein stoichiometry (subunit composition) across all biological assemblies in the PDB archive, we have developed an efficient algorithm with which to characterize symmetry, extending earlier work by Levy (26).”
Sequence-similar, structure-dissimilar protein pairs in the PDB (2007, background): “34 (4) Using global RMSD as a measure of dissimilarity under-states relatively local changes in larger proteins.”
Flexible backbone assembly and refinement of symmetrical homomeric complexes (2018, background): “Despite an estimated 50-70% of proteins being symmetric homomers (Levy et al., 2006), less than 40% of proteins in the Protein Data Bank (Berman et al., 2000) are symmetric (as of June 2018).”
ComplexContact: a web server for inter-protein contact prediction using deep learning (2018, background): “As shown in Figure 2, on a much larger benchmark (of 4479 heterodimers) extracted from 3D complex (37), Com-plexContact outperforms Gremlin by a large margin regardless of the species of the test dimers.”