MODEL/ENDMDL records in PDB X-ray crystal structures

Over the years, I have always been using the PDB format for nucleic acid structures. Naturally I've thought that I know the format well, especially the "Coordinate Section." According to the PDB documentation,

MODEL/ENDMDL records are used only when more than one structure is presented in the entry, as is often the case with NMR entries.

In my experience, I have always connected the MODEL/ENDMDL pair only with the different models in an NMR entry. However, I was recently bitten by a subtlety in PDB format that is related to the MODEL/ENDMDL records in X-ray crystal structures which contain more than one asymmetric unit in their biological assembly.

As always, the point is best illustrated with an example – here I am using the four-stranded DNA Holliday junction X-ray crystal structure (1zf4/ud0061) solved by Ho and colleagues [PNAS 2005 May 17;102(20):7157-62]. As shown in the NDB website, the asymmetric unit of 1zf4/ud0061 contains only two chains; it is the biological assembly that has the four-stranded DNA junction.

I downloaded the biological assembly coordinates (in PDB format) from the NDB (named it '1zf4.pdb'), and ran blocview on it: blocview -i=1zf4.png 1zf4.pdb. However, the generated image [see Figure (A) below] has only half of what expected – as if the downloaded file contains only coordinates of an asymmetric unit. The mystery was gone when I checked the PDB file and realized that the MODEL/ENDMDL records now also apply to X-ray crystal structures to delineate symmetric-related units. Since 3DNA is designed to handle only one structure – it stops processing whenever an END or ENDMDL record is encountered. Simply change each 'ENDMDL' record to ' ENDMDL' (i.e., adding a space, or any character, for that matter) and run blocview again will get the expected image [Figure (B)].

Note that by default, RasMol also only displays the first model in a PDB file. To see multiple structures, the option '-nmrpdb' must be specified in the command line.