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tutorials:structural_functional_analysis [2012/03/29 11:10] jon |
tutorials:structural_functional_analysis [2015/09/21 16:05] (current) hafsa [The CATHEDRAL Server] |
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| ==== The CATHEDRAL Server ==== | ==== The CATHEDRAL Server ==== | ||
| - | First of all, you need to retrieve all the domains present in FtsA. You can use the CATHEDRAL server to do this. The CATHEDRAL server employs a structural comparison algorithm to compare the query structure against known domains in the CATH database, which means you can also use it to try and identify a unknown protein by comparing it with all known structures in CATH. You submit the protein for analysis at [[http://beta.cathdb.info/cgi-bin/CathedralServer.pl|CATHEDRAL search page]]. You can download the PDB file for 1e4f from the [[http://www.rcsb.org/pdb/download/download.do|PDB server]] but, in this case, as 1e4f is known to already exist in the CATH database you can enter the code 1e4f directly into the query box. Then wait for the results to arrive and answer the questions below. | + | First of all, you need to retrieve all the domains present in FtsA. You can use the CATHEDRAL server to do this. The CATHEDRAL server employs a structural comparison algorithm to compare the query structure against known domains in the CATH database, which means you can also use it to try and identify a unknown protein by comparing it with all known structures in CATH. You submit the protein for analysis at [[http://v3-4.cathdb.info/cgi-bin/search.pl?search_text=|CATHEDRAL search page]]. You can download the PDB file for 1e4f from the [[http://www.rcsb.org/pdb/download/download.do|PDB server]] but, in this case, as 1e4f is known to already exist in the CATH database you can enter the code 1e4f directly into the query box. Then wait for the results to arrive and answer the questions below. |
| <box Info|'''CATHEDRAL Results (shortcut)'''> | <box Info|'''CATHEDRAL Results (shortcut)'''> | ||
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| </box> | </box> | ||
| - | To find the domain in CATH, enter the domain code (i.e. 1e4f followed by the chain ID and domain ID) into the search box [[http://www.cathdb.info|on the CATH website]] and look at the result. If you look at the homologous superfamily level (the H-level) you will see that the domain has the code 3.30.420.40. Click on this level to view the structures of other known domains from this homologous superfamily. | + | To find the domain in CATH, enter the domain code (i.e. 1e4f followed by the chain ID and domain ID) into the search box [[http://update.cathdb.info/|Click Here]] and look at the result. If you look at the homologous superfamily level (the H-level) you will see that the domain has the code 3.30.420.40. Click on this level to view the structures of other known domains from this homologous superfamily. |
| <box Question|Question> | <box Question|Question> | ||
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| We're going to start with the 1e4fT04 domain you have been investigating. You will take other examples from the superfamily later and make observations from Gene3D. | We're going to start with the 1e4fT04 domain you have been investigating. You will take other examples from the superfamily later and make observations from Gene3D. | ||
| - | Follow this link to [[http://gene3d.biochem.ucl.ac.uk/|Gene3D]]. The Gene3D front page consists of several search options, to retrieve different data types (proteins, superfamily summaries, genome summaries, etc.). For now go use the protein retrieval search option by entering '1e4fT' into the search box (or follow this shortcut [[http://gene3d.biochem.ucl.ac.uk/proteins/?keywords=1e4ft|Click Here]]). | + | Follow this link to [[http://gene3d.biochem.ucl.ac.uk/|Gene3D]]. The Gene3D front page consists of several search options, to retrieve different data types (proteins, superfamily summaries, genome summaries, etc.). For now go use the protein retrieval search option by entering '1e4fT' into the search box (or follow this shortcut [[http://gene3d.biochem.ucl.ac.uk/search?sterm=1e4fT&mode=ppi|Click Here]]). |
| A page is return which contains a series of tabs containing structural and functional information related to 1e4fT. Compare the HMM-based predictions (CATH_HMM) to the Pfam domain assignments. Pfam families are normally derived from analysis of sequences rather than structures and so can often contain multiple structural domains that commonly co-occur. | A page is return which contains a series of tabs containing structural and functional information related to 1e4fT. Compare the HMM-based predictions (CATH_HMM) to the Pfam domain assignments. Pfam families are normally derived from analysis of sequences rather than structures and so can often contain multiple structural domains that commonly co-occur. | ||
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| ==== Heat Shock Chaperones ==== | ==== Heat Shock Chaperones ==== | ||
| - | Next try 1dkgD (or follow this shortcut [[http://gene3d.biochem.ucl.ac.uk/proteins/?keywords=1dkgD|Click Here]]).. From the domain architecture view we can see that the CATH_HMM architectures is quite detailed and complete. | + | Next try 1dkgD (or follow this shortcut [[http://gene3d.biochem.ucl.ac.uk/search?sterm=1dkgD&mode=ppi|Click Here]]).. From the domain architecture view we can see that the CATH_HMM architectures is quite detailed and complete. |
| <box Info|Brief Explanation of Discontinuous Domains> | <box Info|Brief Explanation of Discontinuous Domains> | ||
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| ==== Eukaryotic Hexokinases ==== | ==== Eukaryotic Hexokinases ==== | ||
| - | As an example of this group, search Gene3D with the pdb 1bdg (or follow this shortcut [[http://gene3d.biochem.ucl.ac.uk/proteins/?keywords=1bdg|Click Here]]). The protein is a hexokinase in the parasitic worm //Schistosoma mansoni//. In this section you are going to search a CATH superfamily and restrict the results according to various criteria. | + | As an example of this group, search Gene3D with the pdb 1bdg (or follow this shortcut [[http://gene3d.biochem.ucl.ac.uk/search?sterm=1bdg&mode=protein|Click Here]]). The protein is a hexokinase in the parasitic worm //Schistosoma mansoni//. In this section you are going to search a CATH superfamily and restrict the results according to various criteria. |
| Looking at the domain architecture in the sequence features tab we can see that the protein has two CATH domains, clicking on the CATH domains we see they have different Funfam annotations. | Looking at the domain architecture in the sequence features tab we can see that the protein has two CATH domains, clicking on the CATH domains we see they have different Funfam annotations. | ||
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| For this family you are going to look at interactions. For this you are going to start with the Actin-related protein (arp) with the PDB code 1k8kA. Search this term in the Gene3D | For this family you are going to look at interactions. For this you are going to start with the Actin-related protein (arp) with the PDB code 1k8kA. Search this term in the Gene3D | ||
| - | (or follow this shortcut [[http://gene3d.biochem.ucl.ac.uk/proteins/?keywords=1k8kA|Click Here]]). | + | (or follow this shortcut [[http://gene3d.biochem.ucl.ac.uk/search?sterm=1k8kA&mode=protein|Click Here]]). |
| <box Question|Question> | <box Question|Question> | ||
