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EPPIC assembly graph corresponding to the D3 symmetric assembly of PDB structure 4ht5. Nodes are protein molecules and edges interfaces between them. Different edge colors represent distinct modes of binding.

EPPIC (Evolutionary Protein-Protein Interface Classifier) provides value-added information about biological assemblies in the PDB. This web server classifies interfaces present in protein crystals to distinguish biological interfaces from crystal contacts. The latest version of EPPIC (v3) now enumerates all possible symmetric assemblies with a prediction of the most likely assembly based on probabilistic scores from pairwise evolutionary scoring. EPPIC is now fully hosted and supported at RCSB PDB.

A detailed description was recently published:

S Bliven, A Lafita, A Parker, G Capitani, JM Duarte (2018) Automated evaluation of quaternary structures from protein crystals. PLoS Comput Biol 14(4): e1006104. doi: 10.1371/journal.pcbi.1006104

EPPIC was also highlighted in the PLOS BIOLOGUE.

The EPPIC project was initiated by Guido Capitani at the Paul Scherrer Institut. Guido sadly passed away in 2017. He was a good friend and colleague and will be missed.

RCSB PDB News ImageEPPIC assembly graph corresponding to the D3 symmetric assembly of PDB structure 4ht5. Nodes are protein molecules and edges interfaces between them. Different edge colors represent distinct modes of binding.

These electron density maps can be viewed in 3D at rcsb.org using NGL. Both 2fo-fc and fo-fc maps are available, and can be displayed at different sigma levels and styles. Shown: Electron density 2fo-fc map for PDB structure 1CBS centered around Retinoic Acid (REA) at 1 sigma contour level.

Electron density maps combine the structural model (coordinates) and experimentally-collected data from an X-ray structure determination and serve to represent the fit of the model to the data. There are two types of electron density maps commonly used by researchers: 2fo-fc and fo-fc. The fo-fc map (also called a difference or omit map) map shows what has been overrepresented or not accounted for by the model, while the 2fo-fc map includes the fo-fc map and electron density around the model.

These two maps are then used to correct the model when possible. Areas of poor electron density can be viewed in even in the best quality structures. This may represent sections of the model that exist in multiple conformations, as seen in long side chains or surface loops of the model.

DSN6 format files (for use with programs including O, pymol, JSmol/Jmol, and Chimera) and MTZ format phase files (for CCP4) are available for download from from Structure Summary pages at rcsb.org and from edmaps.rcsb.org/persist. Additional documentation is available.

Learn more about “Structure Factors and Electron Density” at PDB-101.