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SWISS-MODEL Homology Modelling Report |
Model Building Report
This document lists the results for the homology modelling project "ORF9b protein (ORF9b) | P0DTD2" submitted to SWISS-MODEL workspace on May 5, 2023, 9:34 p.m..The submitted primary amino acid sequence is given in Table T1.
If you use any results in your research, please cite the relevant publications:
- Waterhouse, A., Bertoni, M., Bienert, S., Studer, G., Tauriello, G., Gumienny, R.,
Heer, F.T., de Beer, T.A.P., Rempfer, C., Bordoli, L., Lepore, R., Schwede, T.
SWISS-MODEL: homology modelling of protein structures and complexes.
Nucleic Acids Res. 46(W1), W296-W303 (2018).
- Bienert, S., Waterhouse, A., de Beer, T.A.P., Tauriello, G., Studer,
G., Bordoli, L., Schwede, T. The SWISS-MODEL Repository - new features and
functionality. Nucleic Acids Res. 45, D313-D319 (2017).
- Studer, G., Tauriello, G., Bienert, S.,
Biasini, M., Johner, N., Schwede, T. ProMod3 - A versatile homology
modelling toolbox. PLOS Comp. Biol. 17(1), e1008667 (2021).
- Studer, G., Rempfer, C., Waterhouse, A.M.,
Gumienny, G., Haas, J., Schwede, T. QMEANDisCo - distance constraints
applied on model quality estimation. Bioinformatics 36, 1765-1771 (2020).
- Bertoni, M., Kiefer, F., Biasini, M., Bordoli, L.,
Schwede, T. Modeling protein quaternary structure of homo- and
hetero-oligomers beyond binary interactions by homology. Scientific
Reports 7 (2017).
Results
The SWISS-MODEL template library (SMTL version 2023-05-05, PDB release 2023-04-28) was searched with for evolutionary related structures matching the target sequence in Table T1. For details on the template search, see Materials and Methods. Overall 33 templates were found (Table T2).
Models
The following models were built (see Materials and Methods "Model Building"):
Model #02 |
File | Built with | Oligo-State | Ligands | GMQE | QMEANDisCo Global |
---|---|---|---|---|---|---|
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PDB | ProMod3 3.3.0 | homo-dimer (matching prediction) |
None
|
0.64 | 0.66 ± 0.06 |
|
Template | Seq Identity | Oligo-state | QSQE | Found by | Method | Resolution | Seq Similarity | Range | Coverage | Description |
---|---|---|---|---|---|---|---|---|---|---|
6z4u.1.A | 100.00 | homo-dimer | 0.66 | HHblits | X-ray | 1.95Å | 0.60 | 1 - 97 | 1.00 | Protein 9b |
Excluded ligands
Ligand Name.Number | Reason for Exclusion | Description |
---|---|---|
15P.1 | Not biologically relevant. | POLYETHYLENE GLYCOL (N=34) |
Target MDPKISEMHPALRLVDPQIQLAVTRMENAVGRDQNNVGPKVYPIILRLGSPLSLNMARKTLNSLEDKAFQLTPIAVQMTK
6z4u.1.A MDPKISEMHPALRLVDPQIQLAVTRMENAVGRDQNNVGPKVYPIILRLGSPLSLNMARKTLNSLEDKAFQLTPIAVQMTK
Target LATTEELPDEFVVVTVK
6z4u.1.A LATTEELPDEFVVVTVK
Target MDPKISEMHPALRLVDPQIQLAVTRMENAVGRDQNNVGPKVYPIILRLGSPLSLNMARKTLNSLEDKAFQLTPIAVQMTK
6z4u.1.B MDPKISEMHPALRLVDPQIQLAVTRMENAVGRDQNNVGPKVYPIILRLGSPLSLNMARKTLNSLEDKAFQLTPIAVQMTK
Target LATTEELPDEFVVVTVK
6z4u.1.B LATTEELPDEFVVVTVK
Model #01 |
File | Built with | Oligo-State | Ligands | GMQE | QMEANDisCo Global |
---|---|---|---|---|---|---|
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PDB | ProMod3 3.3.0 | homo-dimer (requested by user) |
1 x D10: DECANE;
|
0.52 | 0.61 ± 0.07 |
|
Template | Seq Identity | Oligo-state | QSQE | Found by | Method | Resolution | Seq Similarity | Range | Coverage | Description |
---|---|---|---|---|---|---|---|---|---|---|
2cme.2.A | 81.33 | homo-dimer | 0.54 | BLAST | X-ray | 2.80Å | 0.53 | 10 - 97 | 0.77 | HYPOTHETICAL PROTEIN 5 |
Included Ligands
Ligand | Description |
---|---|
1 x D10 | DECANE |
Target MDPKISEMHPALRLVDPQIQLAVTRMENAVGRDQNNVGPKVYPIILRLGSPLSLNMARKTLNSLEDKAFQLTPIAVQMTK
2cme.2.A ---------PALHLVDPQIQLTIT-------------DPKVYPIILRLGSNLSLSMARRNLDSLEARAFQSTPIVVQMTK
Target LATTEELPDEFVVVTVK
2cme.2.A LATTEELPDEFVVVTAK
Target MDPKISEMHPALRLVDPQIQLAVTRMENAVGRDQNNVGPKVYPIILRLGSPLSLNMARKTLNSLEDKAFQLTPIAVQMTK
2cme.2.B ---------PALHLVDPQIQLTIT-------------DPKVYPIILRLGSNLSLSMARRNLDSLEARAFQSTPIVVQMTK
Target LATTEELPDEFVVVTVK
2cme.2.B LATTEELPDEFVVVTAK
Materials and Methods
Template Search
Template search with has been performed against the SWISS-MODEL template library (SMTL, last update: 2023-05-05, last included PDB release: 2023-04-28).
Model Building
Models are built based on the target-template alignment using ProMod3 (Studer et al.). Coordinates which are conserved between the target and the template are copied from the template to the model. Insertions and deletions are remodelled using a fragment library. Side chains are then rebuilt. Finally, the geometry of the resulting model is regularized by using a force field.
Model Quality Estimation
The global and per-residue model quality has been assessed using the QMEAN scoring function (Studer et al.).
Ligand Modelling
Ligands present in the template structure are transferred by homology to the model when the following criteria are met: (a) The ligands are annotated as biologically relevant in the template library, (b) the ligand is in contact with the model, (c) the ligand is not clashing with the protein, (d) the residues in contact with the ligand are conserved between the target and the template. If any of these four criteria is not satisfied, a certain ligand will not be included in the model. The model summary includes information on why and which ligand has not been included.
Oligomeric State Conservation
The quaternary structure annotation of the template is used to model the target sequence in its oligomeric form. The method (Bertoni et al.) is based on a supervised machine learning algorithm, Support Vector Machines (SVM), which combines interface conservation, structural clustering, and other template features to provide a quaternary structure quality estimate (QSQE). The QSQE score is a number between 0 and 1, reflecting the expected accuracy of the interchain contacts for a model built based a given alignment and template. Higher numbers indicate higher reliability. This complements the GMQE score which estimates the accuracy of the tertiary structure of the resulting model.
References
- BLAST
Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., Madden, T.L. BLAST+: architecture and applications. BMC Bioinformatics 10, 421-430 (2009). - HHblits
Steinegger, M., Meier, M., Mirdita, M., Vöhringer, H., Haunsberger, S. J., Söding, J. HH-suite3 for fast remote homology detection and deep protein annotation. BMC Bioinformatics 20, 473 (2019).
Table T1:
Primary amino acid sequence for which templates were searched and models were built.
Table T2:
Template | Seq Identity | Oligo-state | QSQE | Found by | Method | Resolution | Seq Similarity | Coverage | Description |
---|---|---|---|---|---|---|---|---|---|
7ye7.1.B | 100.00 | homo-dimer | 0.70 | HHblits | X-ray | 2.95Å | 0.60 | 1.00 | ORF9b protein |
6z4u.1.A | 100.00 | homo-dimer | 0.66 | HHblits | X-ray | 1.95Å | 0.60 | 1.00 | Protein 9b |
7ye8.1.A | 100.00 | homo-dimer | 0.69 | HHblits | X-ray | 3.01Å | 0.60 | 1.00 | ORF9b protein |
6z4u.1.B | 100.00 | homo-dimer | 0.65 | HHblits | X-ray | 1.95Å | 0.60 | 1.00 | Protein 9b |
7ye7.1.A | 100.00 | homo-dimer | 0.69 | HHblits | X-ray | 2.95Å | 0.60 | 1.00 | ORF9b protein |
7ye7.2.A | 100.00 | homo-dimer | 0.66 | HHblits | X-ray | 2.95Å | 0.60 | 1.00 | ORF9b protein |
2cme.2.A | 80.26 | homo-dimer | 0.54 | HHblits | X-ray | 2.80Å | 0.53 | 0.78 | HYPOTHETICAL PROTEIN 5 |
2cme.2.A | 81.33 | homo-dimer | 0.54 | BLAST | X-ray | 2.80Å | 0.53 | 0.77 | HYPOTHETICAL PROTEIN 5 |
2cme.1.A | 78.21 | monomer | - | HHblits | X-ray | 2.80Å | 0.52 | 0.80 | HYPOTHETICAL PROTEIN 5 |
2cme.1.B | 78.48 | monomer | - | HHblits | X-ray | 2.80Å | 0.52 | 0.81 | HYPOTHETICAL PROTEIN 5 |
2cme.3.A | 79.22 | monomer | - | HHblits | X-ray | 2.80Å | 0.52 | 0.79 | HYPOTHETICAL PROTEIN 5 |
2cme.1.A | 80.26 | monomer | - | BLAST | X-ray | 2.80Å | 0.53 | 0.78 | HYPOTHETICAL PROTEIN 5 |
2cme.1.B | 80.52 | monomer | - | BLAST | X-ray | 2.80Å | 0.53 | 0.79 | HYPOTHETICAL PROTEIN 5 |
2cme.3.A | 81.33 | monomer | - | BLAST | X-ray | 2.80Å | 0.53 | 0.77 | HYPOTHETICAL PROTEIN 5 |
7kdt.1.B | 100.00 | monomer | - | HHblits | EM | NA | 0.60 | 1.00 | ORF9b protein |
7dhg.1.B | 100.00 | monomer | - | HHblits | X-ray | 2.20Å | 0.60 | 1.00 | ORF9b protein |
The table above shows the top 16 filtered templates. A further 17 templates were found which were considered to be less suitable for modelling than the filtered list.
2apo.1.A, 2aus.1.A, 2aus.2.A, 2ey4.1.A, 2ey4.2.A, 2hvy.1.B, 2rfk.1.D, 3hax.1.A, 3hjw.1.A, 3hjy.1.A, 3lwo.1.A, 3mqk.1.A, 7qep.17.A, 7ye7.2.B, 7ye8.1.B, 7ye8.2.A, 7ye8.2.B