Integrate X-ray structure with missing domains using templates
Dear Modeller users,
I'm trying to build a model of a hetero-dimer starting from an X-ray structure. Each monomer have 3 domains (6 in total). An X-ray structure of part of the complex (two domains of each monomer) exist and I want to complete the model with the two missing domains (one for each monomer). I would use the X-ray of homologous proteins for which all 6 domains are available. Which would be the best approach? I want to keep the X-ray part as frozen as possible, and only model the two missing domains from the template (both structure and orientation in the complex).
Thank you very much in advance for any tips
Stefano
On 2/25/20 7:26 AM, Stefano Motta wrote: > I'm trying to build a model of a hetero-dimer starting from an X-ray > structure. Each monomer have 3 domains (6 in total). An X-ray structure > of part of the complex (two domains of each monomer) exist and I want to > complete the model with the two missing domains (one for each monomer). > I would use the X-ray of homologous proteins for which all 6 domains are > available. Which would be the best approach? I want to keep the X-ray > part as frozen as possible, and only model the two missing domains from > the template (both structure and orientation in the complex).
This should a straightforward application of multiple-template modeling. You may just need to manually modify the alignment if you get conflicts (e.g. don't align the model with the 6-domain template in some regions if it doesn't align well with your X-ray structure).
Ben Webb, Modeller Caretaker
Thanks for your answer. Do you mean that I should remove the 4 domains present in the X-ray of my target protein from the homologous template? I tried this but the resulting model did not preserve the quaternary architecture of the homologous template (the two additional domains were rigidly moved away). I thought a good idea would be to use as input model (inifile) the X-ray structure of my target protein and refine the two additional models using the whole homologous proteins as template. I also defined the selection to model as explained in: https://salilab.org/modeller/9.23/manual/node23.html
Anyway I got the following:
No atoms were read from the specified input PDB file, since the starting residue number and/or chain id in MODEL_SEGMENT (or the alignment file header) was not found; requested starting position: residue number " ", chain " "; atom file name: INI_MOD.pdb
(Where INI_MOD.pdb is the input model defined in inifile) Why did I get this? Thank you very much for your support,
Stefano
Il giorno mar 25 feb 2020 alle ore 22:59 Modeller Caretaker < modeller-care@salilab.org> ha scritto:
> On 2/25/20 7:26 AM, Stefano Motta wrote: > > I'm trying to build a model of a hetero-dimer starting from an X-ray > > structure. Each monomer have 3 domains (6 in total). An X-ray structure > > of part of the complex (two domains of each monomer) exist and I want to > > complete the model with the two missing domains (one for each monomer). > > I would use the X-ray of homologous proteins for which all 6 domains are > > available. Which would be the best approach? I want to keep the X-ray > > part as frozen as possible, and only model the two missing domains from > > the template (both structure and orientation in the complex). > > This should a straightforward application of multiple-template modeling. > You may just need to manually modify the alignment if you get conflicts > (e.g. don't align the model with the 6-domain template in some regions > if it doesn't align well with your X-ray structure). > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org https://salilab.org/modeller/ > Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage >
On 2/25/20 2:33 PM, Stefano Motta wrote: > Thanks for your answer. Do you mean that I should remove the 4 domains > present in the X-ray of my target protein from the homologous template?
No. As you discovered you'll lose information that way. I would just align the two templates together and go from there.
> I thought a good idea would be to use as input > model (inifile) the X-ray structure of my target protein
That won't work (as you saw) since the inifile has to have exactly the same sequence as the final model.
Ben Webb, Modeller Caretaker
> > No. As you discovered you'll lose information that way. I would just > align the two templates together and go from there.
But this means that the four domains for which I have the X-ray of my target would be moved a little and I want to avoid it. Can I tell modeller not to move them?
That won't work (as you saw) since the inifile has to have exactly the > same sequence as the final model.
Indeed I added the two missing domains (manually aligned with the template). In this way my infile has exactly the same residues present in the alignment file for the target sequence, but I expect modeller to refine only the two domains I manually add.
Thank you very much for your support,
Stefano
Il giorno mar 25 feb 2020 alle ore 23:37 Modeller Caretaker < modeller-care@salilab.org> ha scritto:
> On 2/25/20 2:33 PM, Stefano Motta wrote: > > Thanks for your answer. Do you mean that I should remove the 4 domains > > present in the X-ray of my target protein from the homologous template? > > No. As you discovered you'll lose information that way. I would just > align the two templates together and go from there. > > > I thought a good idea would be to use as input > > model (inifile) the X-ray structure of my target protein > > That won't work (as you saw) since the inifile has to have exactly the > same sequence as the final model. > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org https://salilab.org/modeller/ > Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage >
Hi
Did you check the tutorial?
I think this is what you are looking for (at the end)
https://salilab.org/modeller/wiki/Missing%20residues
"Because either automodel or loopmodel will build a comparative model using your input PDB as a template, potentially all of the atoms in your final model could move. If you really don't want the non-missing residues to move, you can override the select_atoms method to select only the missing residues with a script similar to that below"
I hope this helps
OCS
Oscar Conchillo Solé Computational Biology Group Data Center Manager, Sysadmin and Bioinformatics Institut de Biotecnologia i Biomedicina (UAB) mail: ocs@bioinf.uab.es telf:0034 93586 8939; 0034 93581 4431
On 2/25/20 11:45 PM, Stefano Motta wrote: > > No. As you discovered you'll lose information that way. I would just > align the two templates together and go from there. > > > But this means that the four domains for which I have the X-ray of my > target would be moved a little and I want to avoid it. Can I tell > modeller not to move them? > > That won't work (as you saw) since the inifile has to have exactly the > same sequence as the final model. > > > Indeed I added the two missing domains (manually aligned with the > template). In this way my infile has exactly the same residues > present in the alignment file for the target sequence, but I expect > modeller to refine only the two domains I manually add. > > Thank you very much for your support, > > Stefano > > > Il giorno mar 25 feb 2020 alle ore 23:37 Modeller Caretaker > <modeller-care@salilab.org mailto:modeller-care@salilab.org> ha scritto: > > On 2/25/20 2:33 PM, Stefano Motta wrote: > > Thanks for your answer. Do you mean that I should remove the 4 > domains > > present in the X-ray of my target protein from the homologous > template? > > No. As you discovered you'll lose information that way. I would just > align the two templates together and go from there. > > > I thought a good idea would be to use as input > > model (inifile) the X-ray structure of my target protein > > That won't work (as you saw) since the inifile has to have exactly > the > same sequence as the final model. > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org mailto:modeller-care@salilab.org > https://salilab.org/modeller/ > Modeller mail list: > https://salilab.org/mailman/listinfo/modeller_usage > > > > -- > ________________________________________________________________ > > Stefano Motta PhD > > Email: stefano.motta@unimib.it mailto:s.motta17@campus.unimib.it > *Field of study:* Molecular Modeling, and Proteins Molecular Dynamics > > Università degli Studi di Milano Bicocca > Department of Earth and Environmental Sciences > > Piazza dell'Ateneo Nuovo, 1 - 20126, Milano (Italy). > _________________________________________________________________ > > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage
On 2/25/20 2:45 PM, Stefano Motta wrote: > No. As you discovered you'll lose information that way. I would just > align the two templates together and go from there. > > But this means that the four domains for which I have the X-ray of my > target would be moved a little and I want to avoid it. Can I tell > modeller not to move them?
Of course: https://salilab.org/modeller/9.23/manual/node23.html
Ben Webb, Modeller Caretaker
participants (3)
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Modeller Caretaker -
Oscar Conchillo-Sole -
Stefano Motta