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SWISS-MODEL Homology Modelling Report |
Model Building Report
This document lists the results for the homology modelling project "nsp10 / nsp16 hetero-oligomeric complex | P0DTD1 PRO_0000449628, PRO_0000449633" 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 sequences in Table T1. For details on the template search, see Materials and Methods. Overall 43 templates were found (Table T2).
Models
The following models were 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 | hetero-1-1-mer |
2 x BDF: beta-D-fructopyranose;
1 x SAM: S-ADENOSYLMETHIONINE; 2 x ZN: ZINC ION; |
0.94 | 0.86 ± 0.05 |
|
Template | Seq Identity | Oligo-state | QSQE | Found by | Method | Resolution | Seq Similarity | Range | Coverage | Description |
---|---|---|---|---|---|---|---|---|---|---|
6w4h.1 | 100.00 | hetero-1-1-mer | - | HHblits | X-ray | 1.80Å | 0.63 | A: 1-298 B: 18-133 | 1.00 | 2'-O-methyltransferase Non-structural protein 10 |
Included Ligands
Ligand | Description |
---|---|
2 x BDF | beta-D-fructopyranose |
1 x SAM | S-ADENOSYLMETHIONINE |
2 x ZN | ZINC ION |
Excluded ligands
Ligand Name.Number | Reason for Exclusion | Description |
---|---|---|
ACT.3 | Not biologically relevant. | ACETATE ION |
ACT.4 | Not biologically relevant. | ACETATE ION |
SO3.1 | Not in contact with model. | SULFITE ION |
Target SSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAP
6w4h.1.A SSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAP
Target GTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFIQQK
6w4h.1.A GTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFIQQK
Target LALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLS
6w4h.1.A LALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLS
Target SYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN
6w4h.1.A SYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN
Target AGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFGGASCCLYCRCH
6w4h.1.B AGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFGGASCCLYCRCH
Target IDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQ
6w4h.1.B IDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQ
Model #02 |
File | Built with | Oligo-State | Ligands | GMQE | QMEANDisCo Global |
---|---|---|---|---|---|---|
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PDB | ProMod3 3.3.0 | hetero-1-1-mer |
1 x SAH: S-ADENOSYL-L-HOMOCYSTEINE;
2 x ZN: ZINC ION; |
0.89 | 0.83 ± 0.05 |
|
Template | Seq Identity | Oligo-state | QSQE | Found by | Method | Resolution | Seq Similarity | Range | Coverage | Description |
---|---|---|---|---|---|---|---|---|---|---|
2xyq.1 | 95.13 | hetero-1-1-mer | 0.92 | HHblits | X-ray | 2.00Å | 0.61 | A: 1-289 B: 10-131 | 0.94 | PUTATIVE 2'-O-METHYL TRANSFERASE NON-STRUCTURAL PROTEIN 10 |
Included Ligands
Ligand | Description |
---|---|
1 x SAH | S-ADENOSYL-L-HOMOCYSTEINE |
2 x ZN | ZINC ION |
Excluded ligands
Ligand Name.Number | Reason for Exclusion | Description |
---|---|---|
CL.1 | Not in contact with model. | CHLORIDE ION |
CL.2 | Not biologically relevant. | CHLORIDE ION |
MG.6 | Not in contact with model. | MAGNESIUM ION |
NA.4 | Not in contact with model. | SODIUM ION |
NA.5 | Not biologically relevant. | SODIUM ION |
Target SSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAP
2xyq.1.A ASQAWQPGVAMPNLYKMQRMLLEKCDLQNYGENAVIPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAP
Target GTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFIQQK
2xyq.1.A GTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPRTKHVTKENDSKEGFFTYLCGFIKQK
Target LALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLS
2xyq.1.A LALGGSIAVKITEHSWNADLYKLMGHFSWWTAFVTNVNASSSEAFLIGANYLGKPKEQIDGYTMHANYIFWRNTNPIQLS
Target SYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN
2xyq.1.A SYSLFDMSKFPLKLRGTAVMSLKENQINDMIYSLLEKGRLIIRENNRVV---------
Target AGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFGGASCCLYCRCH
2xyq.1.B ---------NSTVLSFCAFAVDPAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFGGASCCLYCRCH
Target IDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQ
2xyq.1.B IDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLRNTVCTVCGMWKGYGCSCD--------
Materials and Methods
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 sequences for which templates were searched and models were built.
TTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQ
NDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNAS
SSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN
Table T2:
Template | Seq Identity | Oligo-state | QSQE | Found by | Method | Resolution | Seq Similarity | Coverage | Description |
---|---|---|---|---|---|---|---|---|---|
7jyy.1 | 100.00 | hetero-1-1-mer | 0.99 | HHblits | X-ray | 2.05Å | 0.63 | 1.00 | 2'-O-methyltransferase; Non-structural protein 10 |
8bzv.1 | 100.00 | hetero-1-1-mer | 0.99 | HHblits | X-ray | 1.80Å | 0.63 | 1.00 | 2'-O-methyltransferase nsp16; Non-structural protein 10 |
7l6t.1 | 100.00 | hetero-1-1-mer | 0.98 | HHblits | X-ray | 1.78Å | 0.63 | 1.00 | 2'-O-methyltransferase; Non-structural protein 10 |
3r24.1 | 94.39 | hetero-1-1-mer | 0.97 | BLAST / HHblits | X-ray | 2.00Å | 0.61 | 0.98 | 2'-O-methyl transferase; Non-structural protein 10 and Non-structural protein 11 |
2xyq.1 | 95.13 | hetero-1-1-mer | 0.92 | HHblits | X-ray | 2.00Å | 0.61 | 0.94 | PUTATIVE 2'-O-METHYL TRANSFERASE; NON-STRUCTURAL PROTEIN 10 |
The table above shows the top 5 filtered templates. A further 37 templates were found which were considered to be less suitable for modelling than the filtered list.
2xyq.1, 5yn5.1, 6w4h.1, 6w61.1, 6w75.1, 6w75.2, 6wjt.1, 6wjt.2, 6wkq.1, 6wkq.2, 6wks.1, 6wq3.1, 6wrz.1, 6wvn.1, 6xkm.1, 6yz1.1, 7bq7.1, 7c2i.1, 7c2j.1, 7jhe.1, 7jib.1, 7jpe.1, 7jyy.2, 7jz0.1, 7jz0.2, 7koa.1, 7l6r.1, 7lw3.1, 7lw4.1, 7nh7.1, 7r1t.1, 7r1u.1, 7ult.1, 7ult.2, 8bsd.1, 8c5m.1, 8oto.1