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SWISS-MODEL Homology Modelling Report |
Model Building Report
This document lists the results for the homology modelling project "Non-structural protein 2 (nsp2) | P0DTD1 PRO_0000449620" submitted to SWISS-MODEL workspace on May 5, 2023, 9:33 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 57 templates were found (Table T2).
Models
The following model was built (see Materials and Methods "Model Building"):
Model #01 |
File | Built with | Oligo-State | Ligands | GMQE | QMEANDisCo Global |
---|---|---|---|---|---|---|
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PDB | ProMod3 3.3.0 | monomer |
3 x ZN: ZINC ION;
|
0.88 | 0.84 ± 0.05 |
|
Template | Seq Identity | Oligo-state | QSQE | Found by | Method | Resolution | Seq Similarity | Range | Coverage | Description |
---|---|---|---|---|---|---|---|---|---|---|
7msw.1.A | 100.00 | monomer | 0.00 | HHblits | EM | - | 0.62 | 4 - 638 | 1.00 | Non-structural protein 2 |
Included Ligands
Ligand | Description |
---|---|
3 x ZN | ZINC ION |
Target AYTRYVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLA
7msw.1.A AYTRYVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLA
Target KKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKAT
7msw.1.A KKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKAT
Target CEFCGTENLTKEGATTCGYLPQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKC
7msw.1.A CEFCGTENLTKEGATTCGYLPQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKC
Target AYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFK
7msw.1.A AYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFK
Target QIVESCGNFKVTKGKAKKGAWNIGEQKSILSPLYAFASEAARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQYSLRL
7msw.1.A QIVESCGNFKVTKGKAKKGAWNIGEQKSILSPLYAFASEAARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQYSLRL
Target IDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACEIV
7msw.1.A IDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACEIV
Target GGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYRKCVKSREETGLLMPLKAPKEII
7msw.1.A GGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYRKCVKSREETGLLMPLKAPKEII
Target FLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYCALAPNMMVTNNTFTLKGG
7msw.1.A FLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYCALAPNMMVTNNTFTLKGG
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.
IKTIQPRVEKKKLDGFMGRIRSVYPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKEGATTCGYLPQNAVVKIYCPACHNSEVGP
EHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLNEEIAIILASF
SASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKSILSPLYAFASEAARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQYSLRL
IDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACEIVGGQIVTCAKEIKESVQTFFK
LVNKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYRKCVKSREETGLLMPLKAPKEIIFLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVG
TPVCINGLMLLEIKDTEKYCALAPNMMVTNNTFTLKGG
Table T2:
Template | Seq Identity | Oligo-state | QSQE | Found by | Method | Resolution | Seq Similarity | Coverage | Description |
---|---|---|---|---|---|---|---|---|---|
7msw.1.A | 100.00 | monomer | - | HHblits | EM | NA | 0.62 | 1.00 | Non-structural protein 2 |
7msx.1.A | 100.00 | monomer | - | HHblits | EM | NA | 0.62 | 1.00 | Non-structural protein 2 |
7fac.1.A | 65.09 | monomer | - | BLAST | X-ray | 2.71Å | 0.51 | 0.83 | Non-structural protein 2 |
7fac.1.A | 65.02 | monomer | - | HHblits | X-ray | 2.71Å | 0.50 | 0.82 | Non-structural protein 2 |
7exm.3.A | 100.00 | monomer | - | BLAST | X-ray | 1.96Å | 0.64 | 0.43 | Non-structural protein 2 |
7exm.3.A | 100.00 | monomer | - | HHblits | X-ray | 1.96Å | 0.64 | 0.43 | Non-structural protein 2 |
7exm.2.A | 100.00 | monomer | - | BLAST | X-ray | 1.96Å | 0.64 | 0.43 | Non-structural protein 2 |
7exm.2.A | 100.00 | monomer | - | HHblits | X-ray | 1.96Å | 0.64 | 0.43 | Non-structural protein 2 |
7exm.4.A | 100.00 | monomer | - | HHblits | X-ray | 1.96Å | 0.64 | 0.43 | Non-structural protein 2 |
7exm.1.A | 100.00 | monomer | - | BLAST | X-ray | 1.96Å | 0.64 | 0.43 | Non-structural protein 2 |
7fa1.1.A | 76.45 | monomer | - | BLAST | X-ray | 1.60Å | 0.55 | 0.43 | Non-structural protein 2 |
7fa1.1.A | 76.36 | monomer | - | HHblits | X-ray | 1.60Å | 0.55 | 0.43 | Non-structural protein 2 |
6i7o.46.A | 18.33 | monomer | - | HHblits | EM | NA | 0.26 | 0.09 | Ubiquitin-40S ribosomal protein S31 |
6t4q.30.A | 18.33 | monomer | - | HHblits | EM | NA | 0.26 | 0.09 | Ubiquitin-40S ribosomal protein S31 |
6tb3.31.A | 18.33 | monomer | - | HHblits | EM | NA | 0.26 | 0.09 | Ubiquitin-40S ribosomal protein S31 |
6i7o.107.A | 18.33 | monomer | - | HHblits | EM | NA | 0.26 | 0.09 | Ubiquitin-40S ribosomal protein S31 |
6tnu.31.A | 18.33 | monomer | - | HHblits | EM | NA | 0.26 | 0.09 | Ubiquitin-40S ribosomal protein S31 |
7b7d.31.A | 18.33 | monomer | - | HHblits | EM | NA | 0.26 | 0.09 | Ubiquitin-40S ribosomal protein S31 |
6zvi.1.6 | 18.33 | monomer | - | HHblits | EM | NA | 0.26 | 0.09 | RPS31 isoform 1 |
7nrd.14.A | 18.33 | monomer | - | HHblits | EM | NA | 0.26 | 0.09 | Ubiquitin-40S ribosomal protein S31 |
The table above shows the top 20 filtered templates. A further 37 templates were found which were considered to be less suitable for modelling than the filtered list.
1xjh.1.A, 3jag.76.A, 4u3n.107.A, 4u4o.107.A, 4u4o.32.A, 4u4y.107.A, 4u56.32.A, 4v4n.35.A, 5dat.107.A, 5dat.32.A, 5dc3.32.A, 5it7.76.A, 5jbh.1.K, 5lyb.32.A, 5m1j.34.A, 5mei.117.A, 5ndw.43.A, 5ndw.44.A, 5obm.151.A, 5obm.73.A, 5tga.107.A, 6gsm.1.7, 6gsn.1.O, 6t7t.33.A, 6wdr.1.2, 6zvj.1.7, 7a1g.1.5, 7exm.1.A, 7f52.1.A, 7f52.1.B, 7nrc.79.A, 7tql.1.9, 7zpq.32.A, 7zrs.32.A, 7zuw.32.A, 7zux.32.A, 7zw0.32.A