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 format]]. Unfortunately, information in REMARK 350 is often incorrect (see [https://lists.wwpdb.org/empathy/thread/DNQIHDGCX3E64AJT5ABCTNFW2EJZTGAS discussion of this problem by Roland Dunbrack])<ref name="xudunbrackpreprint" /><ref name="xudunbrack" />. 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.wwpdb.org/empathy/thread/FNLXQHDEEHGFT7UID3WDYWUFFARTMTN7 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.wwpdb.org/empathy/thread/DNQIHDGCX3E64AJT5ABCTNFW2EJZTGAS discussion of this problem by Roland Dunbrack])<ref name="xudunbrackpreprint" /><ref name="xudunbrack" />. 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.wwpdb.org/empathy/thread/FNLXQHDEEHGFT7UID3WDYWUFFARTMTN7 list of examples]. | ||
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*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. | *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 sources generate biological unit models from REMARK 350. Be aware that, as explained above, REMARK 350 may be incorrect. | The following sources generate biological unit models from REMARK 350. Be aware that, as explained above, REMARK 350 may be incorrect. | ||
===FirstGlance in Jmol=== | |||
[http://firstglance.jmol.org FirstGlance] automatically '''displays''' biological unit 1, and enables you to work with it using all of the tools within FirstGlance. However, you '''cannot save the biological unit model in PDB format''', because | [http://firstglance.jmol.org FirstGlance] automatically '''displays''' biological unit 1, and enables you to work with it using all of the tools within FirstGlance. However, you '''cannot save the biological unit model in PDB format''', because | ||
JSmol assigns multiple-character names to duplicated chains. For example, with [[3hyd]], chain A is duplicated to chains A1, A2, A3. These chain names render the pseudo PDB file saved from FirstGlance/JSmol unreadable for many software packages. | JSmol assigns multiple-character names to duplicated chains. For example, with [[3hyd]], chain A is duplicated to chains A1, A2, A3. These chain names render the pseudo PDB file saved from FirstGlance/JSmol unreadable for many software packages. | ||
===MakeMultimer=== | |||
*The MakeMultimer server by Michael Palmer (University of Waterloo, Ontario, Canada) served FirstGlance well from May, 2010, until late 2021, when it was retired. It generated a PDB file in which every chain is assigned a distinct single-character name, and all chains are in a single model. [[#FirstGlance in Jmol|FirstGlance 4.0]], released August 15, 2022, was designed to make external generation of a biological unit PDB file unnecessary. | *The MakeMultimer server by Michael Palmer (University of Waterloo, Ontario, Canada) served FirstGlance well from May, 2010, until late 2021, when it was retired. It generated a PDB file in which every chain is assigned a distinct single-character name, and all chains are in a single model. [[#FirstGlance in Jmol|FirstGlance 4.0]], released August 15, 2022, was designed to make external generation of a biological unit PDB file unnecessary. | ||
===RCSB=== | |||
*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 RCSB (US) [[Protein Data Bank]]. As of April, 2010, "Biological Assemblies" 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 RCSB (US) [[Protein Data Bank]]. As of April, 2010, "Biological Assemblies" were available at the bottom of the list under ''Download Files'' (upper right, near the large [[PDB code]]). | ||
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The [http://dunbrack2.fccc.edu/protcad/ Protein Common Assembly Database] (ProtCAD) a comprehensive structural resource of protein complexes based on presenting clusters of protein assembly structures observed in independent experimental structure determinations of the same or homologous proteins in the Protein Data Bank, with the occurrence in multiple experiments providing validation. | The [http://dunbrack2.fccc.edu/protcad/ Protein Common Assembly Database] (ProtCAD) a comprehensive structural resource of protein complexes based on presenting clusters of protein assembly structures observed in independent experimental structure determinations of the same or homologous proteins in the Protein Data Bank, with the occurrence in multiple experiments providing validation. | ||
===Software: Probable Quaternary Structure Server (PQS)=== | <!--===Software: Probable Quaternary Structure Server (PQS)=== | ||
The [http://pqs.ebi.ac.uk Probable Quaternary Structure Server] (PQS) at the European Bioinformatics Institute examines the inter-chain contacts within protein crystals, and makes an educated guess (using published methods) about which contacts represent co-evolved specific oligomeric contacts, and which are artifacts of crystallization. It was usually correct, but not always. It returns models for what it deduces to be the biological units. There are many possible relationships between the asymmetric unit and the biological units returned by PQS. Examples are given in the discussion of [http://proteinexplorer.org/pqs.htm PQS at ProteinExplorer.Org]. Updates to PQS stopped in August, 2009. In 2010 it is being phased out in favor of PISA (see above). | The [http://pqs.ebi.ac.uk Probable Quaternary Structure Server] (PQS) at the European Bioinformatics Institute examines the inter-chain contacts within protein crystals, and makes an educated guess (using published methods) about which contacts represent co-evolved specific oligomeric contacts, and which are artifacts of crystallization. It was usually correct, but not always. It returns models for what it deduces to be the biological units. There are many possible relationships between the asymmetric unit and the biological units returned by PQS. Examples are given in the discussion of [http://proteinexplorer.org/pqs.htm PQS at ProteinExplorer.Org]. Updates to PQS stopped in August, 2009. In 2010 it is being phased out in favor of PISA (see above).--> | ||
==See Also== | ==See Also== | ||
