|  | 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
--- | --- | --- | --- | --- | --- | ---
| 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
--- | --- | --- | --- | --- | --- | ---
| 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.

AGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIP
TTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQ
SSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDL
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