Fig 1.
Visualizations of the biological assembly for GAD1 from Arabidopsis thaliana [PDB:3HBX], as presented by the EPPIC server.
(a) 3D lattice graph of a full unit cell (http://eppic-web.org/ewui/ewui/latticeGraph?id=3hbx&interfaces=*). The nodes are placed at the centroids of each chain, with edges indicating all interfaces. Many edges extend outside the unit cell due to the periodic nature of the lattice. (b) 2D graph of the hexameric biological assembly, formed by engaging three interface types (interfaces 1-3, 4-6 and 8-13). In both diagrams, nodes are labeled with chain ID and symmetry operator and colored by molecular entity. Edges are numbered sequentially by buried surface area and colored by interface type.
Fig 2.
EPPIC assembly predictions as a confusion matrix of macromolecular sizes.
Tiles are colored as the fraction of predictions (i.e. row normalized). The method achieves 85% precision on the dataset. PDB1 refers to the 1st biological assembly annotation provided by the PDB, in here considered as the true biological assembly.
Fig 3.
Comparison of assembly predictions from EPPIC and PISA on the benchmarking dataset.
On the top right, a pie chart shows the global agreement between EPPIC and PISA. On the bottom left, the confusion matrix of actual (PDB1 annotations) and predicted macromolecular sizes. Tiles colored as a fraction of each EPPIC (blue) and PISA (red) macromolecular size prediction (i.e. row normalized). On the bottom right, the agreement and precision of the methods for each PISA macromolecular size prediction. On the top left, the total number and recall for each macromolecular size in the dataset.
Table 1.
Over and under predictions of EPPIC and PISA in the PDB1 and PiQSi datasets.
Table 2.
Prediction statistics for different oligomeric sizes.
Fig 4.
EPPIC and PISA predictions on the protein assembly dataset as a Venn diagram.
PDB1 refers to the 1st biological assembly annotation provided by the PDB.
Fig 5.
Example of an asymmetric assembly with a heterologous interface.
(a) The crystal lattice of PDB 2VCO as shown by the EPPIC server (http://eppic-web.org/ewui/ewui/latticeGraph?id=2vco&interfaces=1,3). The highlighted tetrameric assembly is the one annotated in the PDB. (b) Schematic 2D representation of a lattice that contains an asymmetric dimer through a heterologous interface but which does not form infinite fibers in the crystal.
Fig 6.
Example of a non-isomorphic assembly in the crystal.
(a) The crystal lattice of PDB 1A99, highlighting the C2 dimer wrapping around the unit cell (http://eppic-web.org/ewui/ewui/latticeGraph?id=1a99&interfaces=7). (b) Schematic 2D representation of a lattice that contains a valid C2 assembly, but which is not isomorphic throughout the crystal.
Fig 7.
Example of an asymmetric assembly with internal pseudo-symmetry in one of the chains.
(a) The ABC transporter (PDB 4FI3). (b) The BtuF periplasmic domain with internal C2 pseudo-symmetry highlighted, including the 2-fold axis of symmetry. The internal symmetry calculation was performed with CE-Symm [35].