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

MDPKISEMHPALRLVDPQIQLAVTRMENAVGRDQNNVGPKVYPIILRLGSPLSLNMARKTLNSLEDKAFQLTPIAVQMTKLATTEELPDEFVVVTVK

## 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