Biological Unit: Difference between revisions
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==Examples== | ==Examples== | ||
<table cellpadding='2' border='1' class='wikitable' align='left' hspace='10'> | |||
<tr><td><center> | <tr><td><center> | ||
Model | Model | ||
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</center></td></tr> | </center></td></tr> | ||
</table> | </table> | ||
* The contacts in this biological unit differ from those in the asymmetric unit. | * The contacts in this biological unit differ from those in the asymmetric unit. | ||
**The "author specified" assembly (in this case the same as the [[asymmetric unit]]) appears unlikely in view of the assembly predicted by [[#Protein Interfaces, Surfaces and Assemblies Server (PISA)|PISA]], which has a much larger buried surface area. | |||
Truncated proteins may form oligomers that are impossible in the native protein. For example, [[1bk5]] (karyopherin alpha) is a truncated part of the natural chain, and forms a dimer that would be prevented by the full-length chain. Dimerization is dependent upon Y397. Mutation Y397D prevents this artifactual dimerization, leading to the monomer [[1ee5]]. | Truncated proteins may form oligomers that are impossible in the native protein. For example, [[1bk5]] (karyopherin alpha) is a truncated part of the natural chain, and forms a dimer that would be prevented by the full-length chain. Dimerization is dependent upon Y397. Mutation Y397D prevents this artifactual dimerization, leading to the monomer [[1ee5]]. | ||
<br clear="left"> | |||
==Visualizing the Biological Unit== | ==Visualizing the Biological Unit== | ||
===Proteopedia=== | |||
On pages titled with a [[PDB code]], Proteopedia shows biological unit 1 by default, with an option to show the asymmetric unit instead. A simple example is [[3hyd]]: biological unit 1 has 4 small peptide chains, while the asymmetric unit has a single chain. A large example is [[1pov]], the polio virus capsid. When biological unit 1 becomes too large for JSmol to handle effectively, it is displayed in [[Molstar|Mol*]] ("[[Molstar]]") instead of [[JSmol]]. An example is the much larger capsid of Eastern Equine Encephalitis Virus, [[6mx4]]. | |||
===FirstGlance in Jmol=== | ===FirstGlance in Jmol=== | ||
FirstGlance in Jmol makes it quick and easy to see the biological unit. The initial display in FirstGlance is automatically "biomolecule 1" from REMARK 350. When it is very large, it will be | FirstGlance in Jmol makes it quick and easy to see, explore, and analyze the biological unit. The initial display in FirstGlance is automatically "biomolecule 1" from REMARK 350. When it is very large, it will be [http://firstglance.jmol.org/notes.htm#simplification simplified to alpha carbon atoms (or a subset thereof)] automatically by FirstGlance. | ||
*Display the molecule in FirstGlance in Jmol: | |||
**Enter the [[PDB code]] in the top search slot at the left edge of any page in Proteopedia. At the page in Proteopedia titled with the PDB code, under <i>Resources</i>, click on the link to FirstGlance. | |||
**Alternatively, go directly to [http://firstglance.jmol.org http://FirstGlance.Jmol.Org] (not http'''s''') and enter the PDB code. | |||
*In the <i>Molecule Information</i> tab (the first/left-most tab), click <i>Biological Unit</i> and follow instructions. When there is more than one biological unit, all will be listed and you can display and analyze each of them. | |||
===How To Show The Biological Unit In Proteopedia=== | ===How To Show The Biological Unit In Proteopedia=== | ||
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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=== | ===FirstGlance in Jmol Limitation=== | ||
[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 internally | ||
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. | ||
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===Software: Protein Interfaces, Surfaces and Assemblies Server (PISA)=== | ===Software: Protein Interfaces, Surfaces and Assemblies Server (PISA)=== | ||
The [http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html Protein Interfaces, Surfaces and Assemblies Server] (PISA) at the European Bioinformatics Institute uses improved methods to predict the biological unit or probable quaternary assembly, compared to its predecessor PQS | The [http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html Protein Interfaces, Surfaces and Assemblies Server] (PISA) at the European Bioinformatics Institute uses improved methods to predict the biological unit or probable quaternary assembly, compared to its predecessor PQS. It examines the contacts that occur in macromolecular crystals used in [[X-ray crystallography]]. It attempts to discriminate between [[crystal contacts]] (artifacts of crystallization) and contacts between chains that have co-evolved to maintain specific oligomeric binding. | ||
===Software: Evolutionary Protein-Protein Interface Classifier (EPPIC)=== | ===Software: Evolutionary Protein-Protein Interface Classifier (EPPIC)=== | ||
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===Software: The Protein Common Assembly Database (ProtCAD)=== | ===Software: The Protein Common Assembly Database (ProtCAD)=== | ||
The [http://dunbrack2.fccc.edu/protcad/ Protein Common Assembly Database] (ProtCAD) a | The [http://dunbrack2.fccc.edu/protcad/ Protein Common Assembly Database] (ProtCAD) is a database of protein complexes based on 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)=== | ||
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==Web Sites== | ==Web Sites== | ||
*[https://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/biological-assemblies Introduction to Biological Assemblies and the PDB Archive] | |||
*[http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html Protein Interfaces, Surfaces and Assemblies Server] (PISA) at the European Bioinformatics Institute. | *[http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html Protein Interfaces, Surfaces and Assemblies Server] (PISA) at the European Bioinformatics Institute. | ||
*[http://pqs.ebi.ac.uk Probable Quaternary Structure Server] (PQS) at the European Bioinformatics Institute. | <!--*[http://pqs.ebi.ac.uk Probable Quaternary Structure Server] (PQS) at the European Bioinformatics Institute. Retired since 2009!--> | ||
*[http://dunbrack.fccc.edu/ProtBuD.php ProtBud, a database of biological unit structures] Offers comparisons and downloads of the results from REMARK 350 vs. PQS. | <!-- protBud appears to be retired. In November, 2022, I cannot find it. -Eric Martz | ||
*[http://dunbrack.fccc.edu/ProtBuD.php ProtBud, a database of biological unit structures] Offers comparisons and downloads of the results from REMARK 350 vs. PQS.--> | |||
*[https://www.molnac.unisa.it/BioTools/cocomaps/ COCOMAPS (bioCOmplexes COntact MAPS)] is a web server for analysis and visualization of the interfaces present in biological complexes, such as protein-protein, protein-DNA and protein-RNA complexes, making use of intermolecular contact maps. | *[https://www.molnac.unisa.it/BioTools/cocomaps/ COCOMAPS (bioCOmplexes COntact MAPS)] is a web server for analysis and visualization of the interfaces present in biological complexes, such as protein-protein, protein-DNA and protein-RNA complexes, making use of intermolecular contact maps. | ||
