Building 3D Structural Alignments
CE and FATCAT are two
pieces of software that compare and align protein 3D structures in PDB
format and can be accessed via a web interface.
In their results, they both provide
In our teaching, we are interested in examining structural alignments,
not with a view to understanding the methods and algorithms used to
build them - rather, as a tool to understanding the interpretation of
sequences alignments in a structural context. Thus, below we provide
only a simple description of how to provide appropriate input to the
software, and how to visualise the resulting alignment in 3D.
- a PDB format file showing the alignment of the two structures
that can be used to examine the structural alignment in PyMOL
- the pairwise sequence alignment corresponding to this structural
Obtaining input PDB files
Both servers can calculate alignments when provided with a pair of PDB
format 3D protein structure files.
There are many different ways to identify files for the set of proteins
you might be interested in e.g.
The links to the PDB files are sometimes tricky to find - the image
below shows the mouse pointer positioned over the icon that leads to
the PDB format file for the record being downloaded.
Note that one PDB file may contain the structures of more than one
protein. The different polymers in such a file are specified by their
"chain" identifiers - for example, in the PDB file 2w8l, there are three polymer chains
If you are comparing and aligning a pair of protein structures, it is
therefore important that you know which chain within the PDB file
corresponds to the protein you want to include in the alignment.
- One Y-family DNA polymerase protein (chain A)
- Two nucleotide chains (chains P and T)
You can determine which proteins correspond to which chains by
examining the PDB file directly, or usually much easier, examining the
corresponding pages describing that particular PDB file at PDB sum or
PDB at the RCSB. The links below lead to the corresponding records for
2w8l from these two resources
These two PDB files are both bacterial adhesins
structures in PyMOL
To highlight the superposition of the aligned structures in the
resulting PyMOL files, try typing the set of commands given below into
interface of the PyMOL window. This will display the two structures in
a similar way as
seen in the image below. This colouring and representation makes a good
starting point to compare the aligned regions of the chains.
Finally, use the instructions on this page PyMOL
to switch on the single-letter amino acid cod sequence view at the top
of the window.
- hide everything
- show cartoon
- color red, chain a
- color cyan, chain b
CE Webserver Pairwise Structural Alignment
Begin with the "CE
calculate two chains" structural alignment query page.
For each of the two chains:
Then click the "Calculate Alignment" button near the top of the page to
begin calculating the alignment.
- specify the local PDB file you want to include in the alignment
- selecting the "User File" radio button
- using the "Choose File" button to specify the location of the
PDB file on your local file system
- in the "Chain ID" field, specify the identifier used for the
chain you want to align from that PDB file
For example, before submitting the two example structures for
the query form would look similar to the image shown below:
The result page shows the pairwise sequence alignment corresponding to
the calculated pairwise structural alignment.
To obtain the file with the two aligned structures in PDB format,
follow the link "Download alignment as a PDB file" below the sequence
NOTE - certain problems associated with loading the aligned
structure files into PyMOL are avoided by making sure that the file is
saved with the suffix .pdf i.e. it is strongly recommended that you
name the file(s) you work with something like "ce_4hhb_a_vs_4hhb_b.pdb"
rather than "ce_4hhb_a_vs_4hhb_b.txt" or similar!
This is the CE
pairwise structural alignment PDB file for the two example
shows the result page for the two example structures.
To view the 3D alignment PDB format file in PyMOL as shown above, you
will need to open the file in a text editor, and delete the following
two lines that are found almost in the middle of the file, re-saving
file under a different name:
This link is to
the CE PDB alignment file for the two example structures modified
in this way.
Alternatively, open the un-modified alignment file in PyMOL and use the
menu to select:
Movie->Show all states
This will also show the two structures at the same time, although
without the cartoon secondary structure representations.
FATCAT Webserver Pairwise Structural Alignment
Beginning with the FATCAT
alignment query form, for each of the two structures:
And example of how the form will look at submission is shown below
- use the "Choose File" button to specify the location of the PDB
record you want to align on your local file system
- in the "Chain" field, specify the name of the chain you want to
align from that PDB file
- in the "Name" field, specify a name that will be assigned to your
structure in the resulting pairwise alignment file
- click "Send Request" to submit your query
Once the results page is returned, follow the link "View the alignment
file" on line "2" of the results to see the pairwise sequence alignment
corresponding to the calculated pairwise structural alignment - this link is to
the corresponding sequence alignment for the two example bacterial
The pairwise structural alignment can be viewed following the link from
the second bullet point of the "4" results "Download the pdb file" - this link is to the
alignment calculated for the two example bacterial adhesin structures.
This link shows
the results page for the two example structures.
The pairwise structure can be loaded directly into PyMOL.
Author: Aidan Budd
Gibson Team Training Pages