|  | SWISS-MODEL Homology Modelling Report

## Model Building Report

This document lists the results for the homology modelling project "2'-O-methyltransferase nsp16 | P0DTD1 PRO_0000449633" 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 1545 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 | monomer | 1 x M7G-A-U-U-A: RNA (5'-D(*(M7G))-R(P*AP*UP*UP*A)-3'); 1 x SAM: S-ADENOSYLMETHIONINE; | 0.94 | 0.88 ± 0.05

Template | Seq Identity | Oligo-state | QSQE | Found by | Method | Resolution | Seq Similarity | Range | Coverage | Description
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
7jyy.1.A | 100.00 | monomer | 0.00 | HHblits | X-ray | 2.05Å | 0.62 | 1 - 298 | 1.00 | 2'-O-methyltransferase

### Included Ligands

Ligand | Description
--- | ---
1 x M7G-A-U-U-A | RNA (5'-D(*(M7G))-R(P*AP*UP*UP*A)-3')
1 x SAM | S-ADENOSYLMETHIONINE

### Excluded ligands

Ligand Name.Number | Reason for Exclusion | Description
--- | --- | ---
CL.5 | Not biologically relevant. | CHLORIDE ION
FMT.6 | Not biologically relevant. | FORMIC ACID
FMT.7 | Not biologically relevant. | FORMIC ACID
FMT.8 | Not biologically relevant. | FORMIC ACID
FMT.9 | Not biologically relevant. | FORMIC ACID
MG.3 | Not in contact with model. | MAGNESIUM ION
NA.4 | Not biologically relevant. | SODIUM ION
ZN.10 | Binding site not conserved. | ZINC ION
ZN.11 | Binding site not conserved. | ZINC ION

    Target    SSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAP
    7jyy.1.A  SSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAP

    Target    GTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFIQQK
    7jyy.1.A  GTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFIQQK

    Target    LALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLS
    7jyy.1.A  LALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLS

    Target    SYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN
    7jyy.1.A  SYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN

### Model #02 | File | Built with | Oligo-State | Ligands | GMQE | QMEANDisCo Global
--- | --- | --- | --- | --- | --- | ---
| PDB | ProMod3 3.3.0 | monomer | 1 x SAM: S-ADENOSYLMETHIONINE; | 0.93 | 0.86 ± 0.05

Template | Seq Identity | Oligo-state | QSQE | Found by | Method | Resolution | Seq Similarity | Range | Coverage | Description
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
7bq7.1.A | 100.00 | monomer | 0.00 | HHblits | X-ray | 2.37Å | 0.62 | 1 - 297 | 1.00 | 2'-O-methyltransferase

### Included Ligands

Ligand | Description
--- | ---
1 x SAM | S-ADENOSYLMETHIONINE

### Excluded ligands

Ligand Name.Number | Reason for Exclusion | Description
--- | --- | ---
ZN.2 | Binding site not conserved. | ZINC ION
ZN.3 | Binding site not conserved. | ZINC ION

    Target    SSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAP
    7bq7.1.A  SSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAP

    Target    GTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFIQQK
    7bq7.1.A  GTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFIQQK

    Target    LALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLS
    7bq7.1.A  LALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLS

    Target    SYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN
    7bq7.1.A  SYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN

## 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.

SSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDL
NDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNAS
SSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN

## Table T2:

Template | Seq Identity | Oligo-state | QSQE | Found by | Method | Resolution | Seq Similarity | Coverage | Description
--- | --- | --- | --- | --- | --- | --- | --- | --- | ---
7l6t.1.A | 100.00 | monomer | - | HHblits | X-ray | 1.78Å | 0.62 | 1.00 | 2'-O-methyltransferase
7l6r.1.A | 100.00 | monomer | - | HHblits | X-ray | 1.98Å | 0.62 | 1.00 | 2'-O-methyltransferase
7jyy.1.A | 100.00 | monomer | - | HHblits | X-ray | 2.05Å | 0.62 | 1.00 | 2'-O-methyltransferase
7jz0.2.A | 100.00 | monomer | - | HHblits | X-ray | 2.15Å | 0.62 | 1.00 | 2'-O-methyltransferase
7jyy.2.A | 100.00 | monomer | - | HHblits | X-ray | 2.05Å | 0.62 | 1.00 | 2'-O-methyltransferase
7ult.2.A | 100.00 | monomer | - | HHblits | X-ray | 1.90Å | 0.62 | 1.00 | 2'-O-methyltransferase
7jz0.1.A | 100.00 | monomer | - | HHblits | X-ray | 2.15Å | 0.62 | 1.00 | 2'-O-methyltransferase
7bq7.1.A | 100.00 | monomer | - | HHblits | X-ray | 2.37Å | 0.62 | 1.00 | 2'-O-methyltransferase
7ult.1.A | 100.00 | monomer | - | HHblits | X-ray | 1.90Å | 0.62 | 1.00 | 2'-O-methyltransferase
3r24.1.A | 93.29 | monomer | - | BLAST | X-ray | 2.00Å | 0.60 | 1.00 | 2'-O-methyl transferase
3r24.1.A | 93.60 | monomer | - | HHblits | X-ray | 2.00Å | 0.60 | 1.00 | 2'-O-methyl transferase
2xyr.1.A | 93.49 | monomer | - | BLAST | X-ray | 2.50Å | 0.60 | 0.98 | PUTATIVE 2'-O-METHYL TRANSFERASE
2xyq.1.A | 93.45 | monomer | - | BLAST | X-ray | 2.00Å | 0.60 | 0.97 | PUTATIVE 2'-O-METHYL TRANSFERASE
2xyr.1.A | 93.47 | monomer | - | HHblits | X-ray | 2.50Å | 0.60 | 0.98 | PUTATIVE 2'-O-METHYL TRANSFERASE
2xyq.1.A | 93.77 | monomer | - | HHblits | X-ray | 2.00Å | 0.60 | 0.97 | PUTATIVE 2'-O-METHYL TRANSFERASE
4ikp.1.B | 13.76 | monomer | - | HHblits | X-ray | 2.00Å | 0.26 | 0.37 | Histone-arginine methyltransferase CARM1
3b3f.1.B | 13.76 | monomer | - | HHblits | X-ray | 2.20Å | 0.26 | 0.37 | Histone-arginine methyltransferase CARM1
2y1w.1.A | 13.89 | monomer | - | HHblits | X-ray | 2.10Å | 0.26 | 0.36 | HISTONE-ARGININE METHYLTRANSFERASE CARM1
4ikp.1.A | 13.76 | monomer | - | HHblits | X-ray | 2.00Å | 0.26 | 0.37 | Histone-arginine methyltransferase CARM1
2y1x.1.A | 13.89 | monomer | - | HHblits | X-ray | 2.40Å | 0.26 | 0.36 | HISTONE-ARGININE METHYLTRANSFERASE CARM1
7fai.1.A | 11.93 | monomer | - | HHblits | X-ray | 2.10Å | 0.25 | 0.37 | Histone-arginine methyltransferase CARM1
3b3g.1.B | 13.76 | monomer | - | HHblits | X-ray | 2.40Å | 0.26 | 0.37 | Histone-arginine methyltransferase CARM1
3b3f.1.A | 13.76 | monomer | - | HHblits | X-ray | 2.20Å | 0.26 | 0.37 | Histone-arginine methyltransferase CARM1

The table above shows the top 23 filtered templates. A further 1,492 templates were found which were considered to be less suitable for modelling than the filtered list.
1aqj.1.A, 1bhj.1.A, 1boo.1.A, 1d2g.1.A, 1d2h.1.A, 1d2h.1.C, 1d2h.1.D, 1db3.1.A, 1dl5.1.A, 1dl5.1.B, 1dus.1.A, 1eiz.1.A, 1ej6.1.A, 1f3l.1.A, 1fbn.1.A, 1fp1.1.A, 1fp2.1.A, 1fpq.1.A, 1g38.1.C, 1g60.1.A, 1g60.1.B, 1g6q.1.A, 1g6q.1.C, 1g6q.1.D, 1g6q.1.E, 1g6q.1.F, 1g8a.1.A, 1i1n.1.A, 1i9g.1.A, 1im8.1.A, 1inl.1.B, 1ixk.1.A, 1iy9.1.A, 1jg1.1.A, 1jg4.1.A, 1jq3.1.A, 1jq3.1.C, 1jqe.1.A, 1jqe.2.A, 1jr4.1.A, 1jsx.1.A, 1khh.1.A, 1kp9.1.A, 1kp9.2.A, 1kpg.2.A, 1kph.1.A, 1kph.4.A, 1kpi.1.A, 1kyz.1.A, 1kyz.1.B, 1kyz.2.A, 1l1e.1.A, 1l1e.2.A, 1l3b.2.C, 1l3c.1.A, 1l3i.1.A, 1mjf.1.A, 1n2x.1.A, 1n2x.2.A, 1nbh.1.A, 1nbh.1.B, 1nbh.1.C, 1nbh.1.D, 1nbi.1.B, 1nkv.1.A, 1nkv.1.B, 1nkv.1.C, 1nt2.1.A, 1nw3.1.A, 1nw7.1.A, 1nw8.1.A, 1o54.1.A, 1o9g.1.A, 1o9h.1.A, 1or8.1.A, 1orh.1.A, 1ori.1.A, 1p1b.1.A, 1p1c.1.A, 1p91.1.A, 1p91.1.B, 1pry.1.A, 1qaq.1.A, 1r18.1.A, 1r6a.1.A, 1r74.1.A, 1ri2.1.A, 1ri4.1.A, 1sb9.1.A, 1sqf.1.A, 1t43.1.A, 1tpy.1.A, 1tw2.1.A, 1tw2.1.B, 1u2z.1.A, 1u2z.3.A, 1uir.1.A, 1vbf.1.A, 1vbf.1.B, 1vbf.2.A, 1vbf.2.B, 1ve3.1.A, 1ve3.2.A, 1vid.1.A, 1vl5.1.A, 1wg8.1.A, 1wg8.2.A, 1ws6.1.A, 1wxw.1.A, 1wxw.1.B, 1wxw.2.A, 1wxx.1.A, 1wzn.1.A, 1x19.1.A, 1x1b.1.A, 1xcj.1.A, 1xds.1.A, 1xds.1.B, 1xdu.1.A, 1xdz.1.A, 1xtp.1.A, 1xva.1.A, 1xxl.1.A, 1y8c.1.A, 1yb2.1.A, 1yub.1.A, 1yzh.1.A, 1z3c.1.A, 1zg3.1.A, 1zga.1.A, 1zgj.1.A, 1zhf.1.A, 1zq9.1.A, 1zq9.1.B, 2adm.1.A, 2aot.1.A, 2aot.2.A, 2aou.1.A, 2aox.1.A, 2as0.1.A, 2as0.1.B, 2avd.1.A, 2avn.1.A, 2b25.1.A, 2b2c.1.A, 2b3t.1.A, 2b78.1.A, 2b9e.1.A, 2bm8.1.D, 2bm8.1.E, 2bm9.1.B, 2bm9.1.F, 2br3.1.A, 2br3.1.B, 2br3.1.F, 2br4.1.A, 2br4.1.B, 2br5.1.A, 2br5.1.D, 2br5.1.F, 2cmg.1.A, 2cmg.1.B, 2cmh.2.A, 2cmh.2.C, 2cmh.2.D, 2cww.1.A, 2dkf.1.A, 2eg5.1.A, 2eju.1.A, 2erc.1.A, 2esr.1.A, 2esr.1.B, 2ex4.1.A, 2f8l.1.A, 2fca.1.A, 2fca.1.B, 2fhp.1.A, 2fhp.2.A, 2fk7.1.A, 2fpo.1.A, 2fpo.2.A, 2fpo.3.A, 2frx.1.A, 2fyt.1.A, 2gh1.1.A, 2gpy.1.A, 2gpy.1.B, 2h00.1.A, 2h00.2.A, 2h00.3.A, 2h1r.1.A, 2hnk.1.A, 2hwk.1.A, 2i6g.1.A, 2i7t.1.A, 2i7v.1.A, 2i7x.1.A, 2ibs.1.C, 2idj.1.A, 2idj.1.D, 2ift.1.A, 2igt.1.A, 2ih4.1.C, 2ip2.1.A, 2ipx.1.A, 2jjq.1.A, 2k4m.1.A, 2kw5.1.A, 2ld4.1.A, 2n47.1.A, 2nnw.1.B, 2np7.1.C, 2nxe.1.A, 2nxe.2.A, 2nxj.1.A, 2nxj.2.A, 2nxn.1.A, 2nyu.1.A, 2o05.1.A, 2o06.1.A, 2o57.1.A, 2o57.1.B, 2o57.2.A, 2o57.2.B, 2oxt.1.A, 2oxt.3.A, 2oy0.1.A, 2ozv.1.A, 2ozv.1.B, 2p1d.1.A, 2p35.1.A, 2p35.1.B, 2p3o.1.A, 2p40.1.A, 2p41.1.A, 2p7h.1.A, 2p8j.1.A, 2pbf.1.A, 2pjd.1.A, 2plw.1.A, 2pss.1.A, 2pss.2.B, 2pwp.1.A, 2pwp.2.A, 2pwy.1.A, 2pwy.1.B, 2px4.1.A, 2px5.1.A, 2pxa.1.A, 2pxx.1.A, 2py6.1.A, 2q41.1.A, 2q41.1.B, 2qe6.1.A, 2qm3.1.A, 2qyo.1.A, 2qyo.1.B, 2r3s.1.A, 2v74.2.A, 2v74.2.B, 2v7e.1.A, 2vdu.1.C, 2vdv.1.A, 2vdw.1.A, 2vs1.1.A, 2vz9.1.A, 2vz9.1.B, 2wa2.1.A, 2wa2.2.A, 2wk1.1.A, 2xbm.1.A, 2xr1.1.A, 2xr1.1.B, 2xva.1.A, 2xva.2.A, 2xva.3.A, 2ycb.1.A, 2ycb.1.B, 2yqz.1.A, 2yr0.2.A, 2ytz.1.A, 2yui.1.A, 2yvl.1.A, 2yx1.3.A, 2yx1.3.B, 2yxd.1.A, 2yxd.1.B, 2yxe.1.A, 2yxe.1.B, 2yxl.1.A, 2zbp.1.A, 2zlb.1.A, 2zsu.1.A, 2zsu.1.B, 2zth.1.A, 2zul.1.A, 2zvj.1.A, 2zzm.1.A, 2zzn.1.A, 2zzn.2.A, 3a26.1.A, 3a27.1.A, 3a4t.1.A, 3a4t.2.A, 3a4y.1.A, 3a7d.1.A, 3a7e.1.A, 3af5.1.A, 3af6.1.A, 3ajd.1.A, 3anx.1.A, 3anx.1.B, 3ay0.1.A, 3ay0.2.A, 3b3j.1.A, 3b7p.1.A, 3b7p.2.A, 3b89.1.A, 3bkw.1.A, 3bkx.1.A, 3bkx.1.B, 3bus.1.A, 3bus.2.A, 3bwc.1.A, 3bwc.1.B, 3bwm.1.A, 3bwy.1.A, 3bxo.1.A, 3c0k.1.A, 3c3p.1.A, 3c3p.1.B, 3c3y.1.A, 3c6k.1.A, 3c6m.1.B, 3cc8.1.A, 3ccf.1.A, 3ccf.2.A, 3cgg.1.A, 3cgg.2.A, 3cjq.3.A, 3cjr.1.A, 3cjt.1.A, 3cjt.2.A, 3ckk.1.A, 3d2l.1.A, 3dh0.1.A, 3dlc.1.A, 3dli.1.A, 3dmh.1.A, 3dou.1.A, 3dp7.1.A, 3dp7.1.B, 3dtn.1.A, 3dxz.1.A, 3e05.1.A, 3e05.1.C, 3e23.1.A, 3e7p.1.A, 3e8s.1.A, 3eey.1.A, 3eey.2.A, 3ege.1.A, 3egi.1.A, 3egi.1.C, 3egv.1.A, 3elw.1.A, 3emd.1.A, 3epp.1.A, 3evb.1.A, 3evg.1.A, 3evz.1.A, 3f4k.1.A, 3fpf.1.A, 3fpf.1.B, 3fpg.1.A, 3fpg.1.B, 3fph.1.A, 3fph.1.B, 3frh.1.A, 3fri.1.A, 3fyc.1.A, 3fyc.2.A, 3fzg.1.A, 3g2m.1.A, 3g2m.1.B, 3g5l.1.A, 3g5l.1.B, 3g5t.1.A, 3g88.1.A, 3g89.1.A, 3g8b.1.A, 3gcz.1.A, 3gdh.1.A, 3gdh.2.A, 3ggd.1.A, 3giw.1.A, 3gjy.1.A, 3gnl.1.A, 3grr.1.A, 3grz.1.A, 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