Abstract
A new scheme has been devised to represent viruses and other biological assemblies with regular noncrystallographic symmetry in the Protein Data Bank (PDB). The scheme describes existing and anticipated PDB entries of this type using generalized descriptions of deposited and experimental coordinate frames, symmetry and frame transformations. A simplified notation has been adopted to express the symmetry generation of assemblies from deposited coordinates and matrix operations describing the required point, helical or crystallographic symmetry. Complete correct information for building full assemblies, subassemblies and crystal asymmetric units of all virus entries is now available in the remediated PDB archive.
Highlights
Recent improvements in structural biology methods have given rise to an increasing body of structural data for biological assemblies composed of tens to thousands of individual protein and/or nucleic acid polymer chains
Protein Data Bank (PDB)-format files automatically generated from remediated mmCIFs hold much of the updated information, including corrected BIOMT matrices to build the full biological assembly and a text description of the regular symmetry
For crystal structures deposited in the crystal frame, noncrystallographic symmetry operations to build the crystal asymmetric unit are provided in MTRIX records
Summary
Recent improvements in structural biology methods have given rise to an increasing body of structural data for biological assemblies composed of tens to thousands of individual protein and/or nucleic acid polymer chains. Several entries contain explicit atom coordinates for larger assemblies, e.g. an icosahedral pentamer, or a full crystal asymmetric unit with one quarter or one half of a full virus capsid In some of these cases coordinates were presumably duplicated for convenient viewing of a particular interface, but in others regular symmetry is only approximate and explicit coordinates are required to represent the unique part of a lower symmetry structure. For the PBCV-1 virus (PDB code 1m4x; Nandhagopal et al, 2002), atomic coordinates are only provided for a small fraction (1/28th) of one icosahedral asymmetric unit containing three chains: a total of 3 Â 28 Â 60 chains and 16 284 240 atoms are required to build the complete capsid In all of these special situations, symmetry-parameter representation and instructions for building complete assemblies from selections of matrix operations, selections of coordinates and/or hierarchical application of transformation operations were defined on a case-by-case basis
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