Biological Unit: Difference between revisions

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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Eric Martz, Eran Hodis, Wayne Decatur, Jaime Prilusky

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 Biological units may be specified in REMARK 350 of the [[PDB file format]]. In some cases, more than one putative biological unit is specified, and downloadable from the [[Protein Data Bank]]. Biological units specified by the author(s) are distinguished from those predicted by software. An example is [[3fad]], which is explained in [http://www.pdb.org/pdb/static.do?p=education_discussion/Looking-at-Structures/bioassembly_tutorial.html Looking at Structures: Introduction to Biological Assemblies and the PDB Archive].
-Atomic coordinates for biological units, when specified by the authors of a published structure in REMARK 350 of the [[PDB file format]], are available from the [[Protein Data Bank]]. As of February, 2010, &quot;biological assemblies&quot; were available at the bottom of the list under ''Download Files'' (upper right, near the large [[PDB code]]).
+Atomic coordinates for biological units, when specified by the authors of a published structure in REMARK 350 of the [[PDB file format]], are available from the [[Protein Data Bank]]. As of April, 2010, &quot;Biological Assemblies&quot; were available at the bottom of the list under ''Download Files'' (upper right, near the large [[PDB code]]).
-One technical problem with the files from RCSB  is that when they contain more than one copy of the asymmetric unit, the chains all have identical names. Also, the additional copies are in separate models, which in some cases complicates visualization.
+One technical problem with the files from RCSB  is that when they contain more than one copy of the asymmetric unit, the chains all have identical names. RCSB offers visualization of these models in Jmol, but it is usually difficult to tell how many chains are present in the biological unit, either in the snapshot (where each chain is colored similarly in a spectral amino- to carboxy-terminal sequence) or in Jmol, where coloring by chain fails to distinguish chains with the same name. Also, the additional copies are in separate models, which may often complicate visualization. In contrast, coordinates for biological units available from PISA or PQS (see below) are in a single model, and each chain is given a distinct name. The best way to determine the number of chains in the coordinates for a biological assembly downloaded
 Sometimes, the specific oligomers were not known at the time the asymmetric unit was published. Also, some authors failed to specify the biological unit even when it was known. Rarely, the specified biological units might be incorrect. For all these reasons, it is advisable to consult sources other than REMARK 350.