Biological Unit: Difference between revisions

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===Unreliability of REMARK 350 in the PDB File Header===

When a structure is deposited in the [[PDB]], the authors are required to specify the biological unit if it is known. This is given in REMARK 350 in the header of the [[PDB file]]. Unfortunately, information in REMARK 350 is often incorrect (see [https://lists.sdsc.edu/pipermail/pdb-l/2013-June/005836.html discussion of this problem by Roland Dunbrack]). There are numerous examples in which the authors state that the biological unit is a monomer in REMARK 350, but provide good experimental evidence in the paper reporting the structure that the biological unit is a dimer. Jose Duarte provided a [https://lists.sdsc.edu/pipermail/pdb-l/2013-June/005834.html list of examples].

When a structure is deposited in the [[PDB]], the authors are required to specify the biological unit if it is known. This is given in REMARK 350 in the header of the [[PDB file format]]. Unfortunately, information in REMARK 350 is often incorrect (see [https://lists.sdsc.edu/pipermail/pdb-l/2013-June/005836.html discussion of this problem by Roland Dunbrack]). There are numerous examples in which the authors state that the biological unit is a monomer in REMARK 350, but provide good experimental evidence in the paper reporting the structure that the biological unit is a dimer. Jose Duarte provided a [https://lists.sdsc.edu/pipermail/pdb-l/2013-June/005834.html list of examples].

~~===REMARK 350 in the PDB File Header===~~

In some cases, more than one putative biological unit is specified in REMARK 350. 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].

~~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].

The following servers generate biological unit models from REMARK 350:

The most reliable way to find out the biological unit is to read the literature and/or contact experts on the molecule in question. Short of such efforts, here are some suggestions:

*When the "author determined" biological unit stated in REMARK 350 has a different number of [[chains]] than the [[asymmetric unit]], the biological unit is more likely to be correct.

*When the "author determined" biological unit stated in REMARK 350 has the same number of chains, in the same conformation, as the asymmetric unit, the stated biological unit is less likely to be correct. There is a significant chance that the authors failed to state a known biological unit in REMARK 350 (see examples above).

*When a biological unit is determined only by software, it is less likely to be correct. The software makes an educated guess based upon the characteristics of the contacts present in the protein crystal, but it is sometimes incorrect.

===Generation of Biological Unit Models from REMARK 350===

The following servers generate biological unit models from REMARK 350. Be careful because, as explained above, REMARK 350 is often incorrect.

====MakeMultimer====

*The [http://watcut.uwaterloo.ca/makemultimer/ MakeMultimer Server] generates a PDB file in which every chain is assigned a distinct single-character name, and all chains are in a single model. MakeMultimer provides direct links for downloading, or for visualizing each biological unit in [[FirstGlance in Jmol]].

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 ===Unreliability of REMARK 350 in the PDB File Header===
-When a structure is deposited in the [[PDB]], the authors are required to specify the biological unit if it is known. This is given in REMARK 350 in the header of the [[PDB file]]. Unfortunately, information in REMARK 350 is often incorrect (see [https://lists.sdsc.edu/pipermail/pdb-l/2013-June/005836.html discussion of this problem by Roland Dunbrack]). There are numerous examples in which the authors state that the biological unit is a monomer in REMARK 350, but provide good experimental evidence in the paper reporting the structure that the biological unit is a dimer. Jose Duarte provided a [https://lists.sdsc.edu/pipermail/pdb-l/2013-June/005834.html list of examples].
+When a structure is deposited in the [[PDB]], the authors are required to specify the biological unit if it is known. This is given in REMARK 350 in the header of the [[PDB file format]]. Unfortunately, information in REMARK 350 is often incorrect (see [https://lists.sdsc.edu/pipermail/pdb-l/2013-June/005836.html discussion of this problem by Roland Dunbrack]). There are numerous examples in which the authors state that the biological unit is a monomer in REMARK 350, but provide good experimental evidence in the paper reporting the structure that the biological unit is a dimer. Jose Duarte provided a [https://lists.sdsc.edu/pipermail/pdb-l/2013-June/005834.html list of examples].
-===REMARK 350 in the PDB File Header===
+In some cases, more than one putative biological unit is specified in REMARK 350. 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].
-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].
-The following servers generate biological unit models from REMARK 350:
+The most reliable way to find out the biological unit is to read the literature and/or contact experts on the molecule in question. Short of such efforts, here are some suggestions:
+*When the "author determined" biological unit stated in REMARK 350 has a different number of [[chains]] than the [[asymmetric unit]], the biological unit is more likely to be correct.
+*When the "author determined" biological unit stated in REMARK 350 has the same number of chains, in the same conformation, as the asymmetric unit, the stated biological unit is less likely to be correct. There is a significant chance that the authors failed to state a known biological unit in REMARK 350 (see examples above).
+*When a biological unit is determined only by software, it is less likely to be correct. The software makes an educated guess based upon the characteristics of the contacts present in the protein crystal, but it is sometimes incorrect.
+===Generation of Biological Unit Models from REMARK 350===
+The following servers generate biological unit models from REMARK 350. Be careful because, as explained above, REMARK 350 is often incorrect.
 ====MakeMultimer====
 *The [http://watcut.uwaterloo.ca/makemultimer/ MakeMultimer Server] generates a PDB file in which every chain is assigned a distinct single-character name, and all chains are in a single model. MakeMultimer provides direct links for downloading, or for visualizing each biological unit in [[FirstGlance in Jmol]].