Primary Citation PubMed: 12411581
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Representation of viruses in the remediated PDB archive.
(2008) Acta Crystallogr D Biol Crystallogr D64
PubMed: 18645236 | PubMedCentral: PMC2677383 | DOI: 10.1107/S0907444908017393
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 chai... s: a total of 3 × 28 × 60 chains and 16 284 240 atoms are required to build the complete capsid.
Complex cases such as the pseudocrystalline symmetry in icosahedral PBCV-1 (PDB entry 1m4x ; Nandhagopal et al. , 2002 ▶ ) can also be represented (Figs. 2 ▶ h and 2 ▶ i and Table 5 ▶ ).
PBCV-1 virus (PDB entry 1m4x ) is the most extreme case: the compressed storage size for the biounit file with 5040 chains is 1000 times bigger than the mmCIF or PDB file with three chains and matrices (0.3 Gb versus 0.3 Mb).
( h ) 1m4x , P. bursaria chorella virus type 1 (PBCV-1) algal virus shell (Nandhagopal et al. , 2002 ▶ ).
Publication Year: 2008
The RCSB Protein Data Bank: new resources for research and education.
(2013) Nucleic Acids Res 41
PubMed: 23193259 | PubMedCentral: PMC3531086 | DOI: 10.1093/nar/gks1200
For biological assemblies, surfaces are generated using the symmetry operation of the space group, which allows the display of even the largest assemblies in the PDB [i.e. the PBCV-1 virus capsid with... 5040 chains, PDB ID 1M4X ( 40 )] on a standard laptop computer.
Publication Year: 2013
PubMed ID is not available.
Published in 2015
The panel in the top left shows the icosahedral structure of the PBCV-1 virus capsid (PDB entry 1M4X) assembled from 1680 copies of the asymmetric unit which is highlighted within the capsid and shown... magnified below it (green).
Publication Year: 2015
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