Michelaɴɢʟo

A VENUS page is created anew on request. A Michelanglo page is stored and can be edited.

Step 2 Configure initial view

Choose how the view of the protein should look like when page first loads (initial view) by either using the view-building interface or by editing the tag directly. See documentation for more information.

Residue numbering mismatch

The residue numbers in the PDB file and those in Uniprot differ for some chains
Click this to make the residues in the structure to match Uniprot (irreversible):

Predicted model

This structure is from Swiss-Model. It is a computational model generated by threaded against a crystallised structure (Swissmodel docs ). It may be incorrect. E.g. missing ligands or broken cysteine bonds.

Engineered residues

The protein contains engineered residues () . Click this to make the residues in the structure to match Uniprot (irreversible):

Initial view

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Selection

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Title

Radius

Tolerance

Show ligands

Orientation

Freeze

The orientation of the protein differs from the stored one above.

Add additional residue selections

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Mutagenesis

The mutations will be in the main structure after the page is created. If the mutated residue is shown in the initial view, it is suggested to use 'clash' focus mode. To show first the wild type structure on page loading but allow the visitor to toggle to a mutation, create a page with no mutations and then add them in the edit menu.

Chain

List of mutations

Chain removal

The asymmetric state of crystal structures do not always reflect the oligomerisation of the protein or there may be unneeded chains.

Chain

Remove waters and ligands

Crystallographic waters are that kept in an ordered position by the protein. Often chemicals that aid in crystallisation are similarly found. Natural ligands will not be removed (cf. blacklist).

Remove waters

Remove crystallisation compounds

Step 3 Create

Create page. Note that chosen initial view cannot be changed once created.

Importance

The region of protein you are after does not appear to have a structure or model in SwissModel.

NB. If you know that a new structure has been released in PDB, message the admin asking for the PDB data to be reparsed.

That a region or whole protein is not solved structurally does not imply that your residue is not important. In the cases of large protein, it is common practice to clone domains as opposed to the whole protein in order to avoid poor protein expression yields —different regions will behave differently, so, again, this is not a valid indicator of the importance of a residue.
Reasons why a given protein is not solved may include:

The protein was never a target for crystallisation —this is typical of protein for which little is known
Whereas other parts of the protein may be crystallised, the region of interest was not cloned because nothing is known about it
The protein or region did not crystallise for technical reasons
The protein or region is membrane bound, which is very hard to express and crystallise
The protein or region is unstructured in an unbound form making it impossible to purify

Disordered

In the plot of the features of the protein, there is a trace labelled 'flexibility'. If your mutation is in a flexible region, it is worth paying particular attention to post translational modifications, which may be listed in the 'Location' box. These are likely to control the levels of the protein.

Model making

There are several servers that model protein for you. First, determine the domains by looking in Uniprot or PDB protein feature view, because no modelling program deals with sequences larger than 500 amino acids —a lazy way of getting the sequence of a region is to click on a range for a domain in Uniprot and changing the numbers in the URL.

I-TASSER is tool that consistently wins a model predicting challenge (CASP), but is slow (2-3 days).
Phyre2 is a lot quicker and also recently they have released a set of over 1,000 computed structures.
EVFold is best for totally unknown structures, because it uses covariance to predict what should be close to what. Namely, Normally parts of a structures are threaded (the residues on the template are simply replace) or are computed ab initio using forcefield calculations.

About the latter, totally unknown genes are wholly imprecise, but the accuracy is increased by using the assumption that residues that change together are likely close. Do note that if you are opting for a model, keep track of what the closest template is and what is the root mean square deviation (low single digit numbers is best) and make it clear with other users that you are using a model.

Michelanglo — VENUS (Multiple)

Assessing the effect of amino acid variants have on structure together

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Mutations

View or analyse a mutation

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Structure