Quaternary Structures


The exercise will introduce the concept of quaternary structure and the role of this state in understanding the function of proteins. Quaternary Structure is defined as that level of form in which units of tertiary structure aggregate to form homo- or hetero-multimers. Consideration of the presence of a quaternary state is important in the understanding of a protein's biological function. The crystallographic experiment on a particular macromolecule yields a set of coordinates that may not necessarily describe the complete molecule under study or may include multiple copies of the molecule. Many multi-subunit proteins crystallize in a manner which allows for the prediction of their quaternary structure by the application of inherent crystal symmetry. For example, a protein which is known to function in a tetrameric (composed of 4 molecules) may crystallize such that the PDB file contains only one deposited molecule. By the application of crystal symmetry, it may be possible to generate the full functional form of the protein.

However, such predictions are based on considerations which include loss of surface area, loss of energy in complex formation etc. As a rule of thumb, any loss of accessible surface which is 10% or more of the total available surface area in the isolated protein is considered to be good. If the predicted gain in energy on complex formation is negative, this indicates that the complex formed will be stable.

Let us look at the following examples:


Example 1: Ferritin

Ferritins are globular proteins that are involved in binding iron molecules and are known to exist as large protein shells made up of 24 subunits containing an hollow core that can store iron (Link to Pfam entry). Look at the atlas page for PDB entry 1DAT from the website http://www.ebi.ac.uk/pdbe/. The crystal structure of the protein contains only one protein chain (designated chain id A on the summary page). Look at the protein molecule from the visualisation page. There is only one chain that is composed of a large number of alpha-helices.



Now look at the Assembly link for this entry. Can you now see the spherical structure of the ferritin molecule ? This spherical form of ferritin was generated by applying simple crystal symmetry inherent in the crystallographic experiment. 


Look at the PQS (Protein Quaternary Structure) entry for this protein by choosing the PISA Details link on the assembly page just below the picture of the complex. This will take you the PDBePISA pages for this entry which provide more information like energetic and surface area calculations which go into the decision making process while automatically assigining quaternary structures. You can also view the structure using the links on the page with Rasmol, First Glance etc. Look at the link on this page which says "Details concerning the results are given in the file 1dat". This file has all the calculations which went into the prediction of this quaternary state.

Example 2: Multiple quaternary structures in the PDB file

Let us consider the opposite scenario to the previous example. In such cases, it is possible that the PDB file may contain the whole quaternary assembly of a protein, or even multiple copies of the same. There are many examples of these and some of them are listed below:

1H2I : RAD52 contains two molecular assemblies of the protein, each of them is 11-meric and all 22 molecules are present in the PDB entry. Look at the PQS entry for this structure here .


Question: What is the loss of accessible surface area in the undecameric complex predicted ?


1B09 : Human C-reactive protein is a member of a family of proteins called pentraxins. These proteins are known to exist in a  pentameric state of 5 non-covalently associated molecules. The crystal structure of 1b09 also contains 5 molecules of the C-reactive protein. Therefore, in this case, there is no need for the expansion of crystal symmetry in order to predict the quaternary structure of the protein. Look at the PQS entry for this protein here.

Question 1: Are there any other structures in the pentraxin family ? (Hint: Look at the Pfam entry for this protein from the Sequence section of the atlas pages).

Example 3: Virus structures

Viral capsid structures are comprised of many hundreds of copies of a few proteins arranged in regular patterns to form the capsid. In the PDB, structures of the viral capsid is represented in the coordinates in the form of a few chains only. Since most capsids have a regular structure, the whole shell of the virus can be generated by using viral and crystal symmetry. In addition, it makes practical sense to only deposit the minimum number of unique chains for a virus in the PDB, since this saves space, and allows the whole capsid to be generated automatically. For example:

PDB entry 1RHI:

Rhinovirus coat protein: The PDB entry for this virus only contains 4 chains, as can be seen from the visualization page for this structure.



The PQS entry for this protein can be seen from this link.

There are many files for this entry and are subsets of the whole viral capsid, and each can be viewed individually. The whole capsid structure is represented by the file 1rh.mmol.