|  | SWISS-MODEL Homology Modelling Report

## Model Building Report

This document lists the results for the homology modelling project "Nucleoprotein (N) | P0DTC9" 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 299 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 | monomer | None | 0.23 | 0.68 ± 0.07

Template | Seq Identity | Oligo-state | QSQE | Found by | Method | Resolution | Seq Similarity | Range | Coverage | Description
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
4ud1.1.A | 55.41 | monomer | 0.00 | BLAST | X-ray | 2.48Å | 0.47 | 40 - 174 | 0.37 | N PROTEIN

### Excluded ligands

Ligand Name.Number | Reason for Exclusion | Description
--- | --- | ---
NH4.1 | Not biologically relevant. | AMMONIUM ION

    Target    MSDNGPQNQRNAPR-ITFGGPSDSTGSNQNGERSGARSKQRRPQGLPNNTASWFTALTQHGKEDLKFPRGQGVPINTNSS
    4ud1.1.A  -----------APRAVSFADNNDITNTNL----SRGRGRNPKPRAAPNNTVSWYTGLTQHGKVPLTFPPGQGVPLNANST

    Target    PDDQIGYYRRATRRIRGGDGKMKDLSPRWYFYYLGTGPEAGLPYGANKDGIIWVATEGALNTPKDHIGTRNPANNAAIVL
    4ud1.1.A  PAQNAGYWRRQDRKINTGNG-IKQLAPRWYFYYTGTGPEAALPFRAVKDGIVWVHEDGATDAPST-FGTRNPNNDSAIVT

    Target    QLPQGTTLPKGFYAEGSRGGSQASSRSSSRSRNSSRNSTPGSSRGTSPARMAGNGGDAALALLLLDRLNQLESKMSGKGQ
    4ud1.1.A  QFAPGTKLPKNFHIE-----------------------------------------------------------------

    Target    QQQGQTVTKKSAAEASKKPRQKRTATKAYNVTQAFGRRGPEQTQGNFGDQELIRQGTDYKHWPQIAQFAPSASAFFGMSR
    4ud1.1.A  --------------------------------------------------------------------------------

    Target    IGMEVTPSGTWLTYTGAIKLDDKDPNFKDQVILLNKHIDAYKTFPPTEPKKDKKKKADETQALPQRQKKQQTVTLLPAAD
    4ud1.1.A  --------------------------------------------------------------------------------

    Target    LDDFSKQLQQSMSSADSTQA
    4ud1.1.A  --------------------

### Model #01 | File | Built with | Oligo-State | Ligands | GMQE | QMEANDisCo Global
--- | --- | --- | --- | --- | --- | ---
| PDB | ProMod3 3.3.0 | monomer | None | 0.21 | 0.74 ± 0.07

Template | Seq Identity | Oligo-state | QSQE | Found by | Method | Resolution | Seq Similarity | Range | Coverage | Description
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
2ofz.1.A | 92.06 | monomer | 0.00 | HHblits | X-ray | 1.17Å | 0.61 | 48 - 173 | 0.30 | Nucleocapsid protein

### Excluded ligands

Ligand Name.Number | Reason for Exclusion | Description
--- | --- | ---
EDO.1 | Not biologically relevant. | 1,2-ETHANEDIOL

    Target    MSDNGPQNQRNAPRITFGGPSDSTGSNQNGERSGARSKQRRPQGLPNNTASWFTALTQHGKEDLKFPRGQGVPINTNSSP
    2ofz.1.A  -----------------------------------------------NTASWFTALTQHGKEELRFPRGQGVPINTNSGP

    Target    DDQIGYYRRATRRIRGGDGKMKDLSPRWYFYYLGTGPEAGLPYGANKDGIIWVATEGALNTPKDHIGTRNPANNAAIVLQ
    2ofz.1.A  DDQIGYYRRATRRVRGGDGKMKELSPRWYFYYLGTGPEASLPYGANKEGIVWVATEGALNTPKDHIGTRNPNNNAATVLQ

    Target    LPQGTTLPKGFYAEGSRGGSQASSRSSSRSRNSSRNSTPGSSRGTSPARMAGNGGDAALALLLLDRLNQLESKMSGKGQQ
    2ofz.1.A  LPQGTTLPKGFYA-------------------------------------------------------------------

    Target    QQGQTVTKKSAAEASKKPRQKRTATKAYNVTQAFGRRGPEQTQGNFGDQELIRQGTDYKHWPQIAQFAPSASAFFGMSRI
    2ofz.1.A  --------------------------------------------------------------------------------

    Target    GMEVTPSGTWLTYTGAIKLDDKDPNFKDQVILLNKHIDAYKTFPPTEPKKDKKKKADETQALPQRQKKQQTVTLLPAADL
    2ofz.1.A  --------------------------------------------------------------------------------

    Target    DDFSKQLQQSMSSADSTQA
    2ofz.1.A  -------------------

### Model #03 | File | Built with | Oligo-State | Ligands | GMQE | QMEANDisCo Global
--- | --- | --- | --- | --- | --- | ---
| PDB | ProMod3 3.3.0 | monomer (matching prediction) | None | 0.18 | 0.60 ± 0.08

Template | Seq Identity | Oligo-state | QSQE | Found by | Method | Resolution | Seq Similarity | Range | Coverage | Description
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
6wzq.2.B | 100.00 | homo-dimer | 0.49 | HHblits | X-ray | 1.45Å | 0.62 | 250 - 364 | 0.28 | Nucleoprotein

### Excluded ligands

Ligand Name.Number | Reason for Exclusion | Description
--- | --- | ---
SO4.1 | Not biologically relevant. | SULFATE ION
SO4.2 | Not biologically relevant. | SULFATE ION
SO4.3 | Not in contact with model. | SULFATE ION

    Target    MSDNGPQNQRNAPRITFGGPSDSTGSNQNGERSGARSKQRRPQGLPNNTASWFTALTQHGKEDLKFPRGQGVPINTNSSP
    6wzq.2.B  --------------------------------------------------------------------------------

    Target    DDQIGYYRRATRRIRGGDGKMKDLSPRWYFYYLGTGPEAGLPYGANKDGIIWVATEGALNTPKDHIGTRNPANNAAIVLQ
    6wzq.2.B  --------------------------------------------------------------------------------

    Target    LPQGTTLPKGFYAEGSRGGSQASSRSSSRSRNSSRNSTPGSSRGTSPARMAGNGGDAALALLLLDRLNQLESKMSGKGQQ
    6wzq.2.B  --------------------------------------------------------------------------------

    Target    QQGQTVTKKSAAEASKKPRQKRTATKAYNVTQAFGRRGPEQTQGNFGDQELIRQGTDYKHWPQIAQFAPSASAFFGMSRI
    6wzq.2.B  ------TKKSAAEASKKPRQKRTATKAYNVTQAFGRRGPEQTQGNFGDQELIRQGTDYKHWPQIAQFAPSASAFFGMSRI

    Target    GMEVTPSGTWLTYTGAIKLDDKDPNFKDQVILLNKHIDAYKTFPPTEPKKDKKKKADETQALPQRQKKQQTVTLLPAADL
    6wzq.2.B  GMEVTPSGTWLTYTGAIKLDDKDPNFKDQVILLNKHIDAYKTFP------------------------------------

    Target    DDFSKQLQQSMSSADSTQA
    6wzq.2.B  -------------------

## 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.

MSDNGPQNQRNAPRITFGGPSDSTGSNQNGERSGARSKQRRPQGLPNNTASWFTALTQHGKEDLKFPRGQGVPINTNSSPDDQIGYYRRATRRIRGGDGK
MKDLSPRWYFYYLGTGPEAGLPYGANKDGIIWVATEGALNTPKDHIGTRNPANNAAIVLQLPQGTTLPKGFYAEGSRGGSQASSRSSSRSRNSSRNSTPG
SSRGTSPARMAGNGGDAALALLLLDRLNQLESKMSGKGQQQQGQTVTKKSAAEASKKPRQKRTATKAYNVTQAFGRRGPEQTQGNFGDQELIRQGTDYKH
WPQIAQFAPSASAFFGMSRIGMEVTPSGTWLTYTGAIKLDDKDPNFKDQVILLNKHIDAYKTFPPTEPKKDKKKKADETQALPQRQKKQQTVTLLPAADL
DDFSKQLQQSMSSADSTQA

## Table T2:

Template | Seq Identity | Oligo-state | QSQE | Found by | Method | Resolution | Seq Similarity | Coverage | Description
--- | --- | --- | --- | --- | --- | --- | --- | --- | ---
8fd5.1.A | 100.00 | monomer | - | HHblits | EM | NA | 0.62 | 1.00 | Nucleoprotein
4ud1.1.A | 55.41 | monomer | - | BLAST | X-ray | 2.48Å | 0.47 | 0.37 | N PROTEIN
7acs.1.A | 100.00 | monomer | - | HHblits | NMR | NA | 0.63 | 0.33 | Nucleoprotein
7sd4.1.A | 100.00 | monomer | - | HHblits | NMR | NA | 0.63 | 0.32 | Nucleoprotein
1ssk.1.A | 92.70 | monomer | - | HHblits | NMR | NA | 0.61 | 0.33 | Nucleocapsid protein
6m3m.2.A | 100.00 | monomer | - | HHblits | X-ray | 2.70Å | 0.63 | 0.32 | Nucleoprotein
6yi3.1.A | 100.00 | monomer | - | HHblits | NMR | NA | 0.63 | 0.33 | Nucleoprotein
1ssk.1.A | 92.37 | monomer | - | BLAST | NMR | NA | 0.61 | 0.31 | Nucleocapsid protein
7act.1.A | 100.00 | monomer | - | HHblits | NMR | NA | 0.63 | 0.33 | Nucleoprotein
6m3m.1.A | 100.00 | monomer | - | HHblits | X-ray | 2.70Å | 0.63 | 0.32 | Nucleoprotein
7cr5.1.A | 100.00 | monomer | - | HHblits | X-ray | 2.08Å | 0.63 | 0.32 | Nucleoprotein
2ofz.1.A | 92.06 | monomer | - | BLAST | X-ray | 1.17Å | 0.61 | 0.30 | Nucleocapsid protein
2ofz.1.A | 92.06 | monomer | - | HHblits | X-ray | 1.17Å | 0.61 | 0.30 | Nucleocapsid protein
6wzq.2.B | 100.00 | homo-dimer | 0.49 | HHblits | X-ray | 1.45Å | 0.62 | 0.28 | Nucleoprotein

The table above shows the top 14 filtered templates. A further 193 templates were found which were considered to be less suitable for modelling than the filtered list.
2btl.1.A, 2btl.2.A, 2bxx.1.A, 2c86.1.A, 2ca1.1.A, 2ca1.1.B, 2cjr.1.A, 2cjr.1.B, 2cjr.2.A, 2cjr.2.B, 2cjr.3.A, 2cjr.3.B, 2cjr.4.A, 2cjr.4.B, 2ge7.1.A, 2ge8.1.A, 2ge8.1.B, 2ge8.2.B, 2gec.1.A, 2gec.1.B, 2gib.1.A, 2jw8.1.A, 2jw8.1.B, 3hd4.1.A, 4j3k.1.A, 4kxj.1.A, 4lm9.1.A, 4lmc.1.A, 4ud1.1.A, 5epw.1.A, 5n4k.1.A, 6ff4.1.T, 6g13.1.A, 6g13.1.B, 6kl2.1.A, 6kl2.1.B, 6kl2.2.A, 6kl5.1.A, 6kl5.2.A, 6kl5.2.B, 6kl6.1.B, 6lnn.1.A, 6lnn.1.B, 6lz6.2.A, 6lz8.2.A, 6m3m.1.A, 6m3m.2.A, 6m3m.3.A, 6m3m.4.A, 6utc.1.A, 6vyo.1.A, 6vyo.1.B, 6vyo.1.C, 6vyo.1.D, 6wji.1.A, 6wji.1.B, 6wji.2.A, 6wji.2.B, 6wji.3.A, 6wji.3.B, 6wkp.1.A, 6wkp.1.B, 6wkp.1.C, 6wkp.1.D, 6wzo.1.A, 6wzo.1.B, 6wzo.2.A, 6wzo.2.B, 6wzq.1.A, 6wzq.1.B, 6wzq.2.A, 6wzq.2.B, 6yi3.1.A, 6yun.1.A, 6yun.1.B, 6zco.1.A, 6zco.1.B, 7abh.1.N, 7acs.1.A, 7act.1.A, 7c22.1.A, 7c22.1.B, 7c22.2.A, 7c22.2.B, 7cdz.1.A, 7cdz.2.A, 7cdz.3.A, 7cdz.4.A, 7ce0.1.A, 7ce0.1.B, 7ce0.2.A, 7ce0.2.B, 7de1.1.A, 7de1.1.B, 7dvq.1.j, 7dyd.1.B, 7dyd.2.B, 7f2b.1.A, 7f2b.1.B, 7f2e.1.A, 7f2e.1.B, 7f2e.2.A, 7f2e.2.B, 7f2e.3.A, 7f2e.3.B, 7f2e.4.A, 7f2e.4.B, 7f2e.5.A, 7f2e.5.B, 7f2e.6.A, 7f2e.6.B, 7n0i.1.A, 7n0i.1.B, 7n0i.2.A, 7n0i.2.B, 7n0i.3.A, 7n0i.3.B, 7n0i.4.A, 7n0i.4.C, 7n0r.1.A, 7n0r.2.A, 7n3c.1.C, 7n3d.1.C, 7n45.1.A, 7nn6.1.A, 7o05.1.A, 7o05.1.B, 7o05.2.A, 7o05.2.B, 7o35.1.A, 7o35.1.B, 7o35.2.A, 7o35.2.B, 7o36.1.A, 7o36.1.B, 7o36.2.A, 7o36.2.B, 7pku.1.B, 7r98.1.A, 7r98.2.A, 7r98.3.A, 7str.1.C, 7sts.1.C, 7sts.2.A, 7sue.1.C, 7sue.2.C, 7sue.3.C, 7sue.4.C, 7uxx.1.A, 7uxx.1.B, 7uxx.2.A, 7uxx.2.B, 7uxx.3.A, 7uxx.3.B, 7uxz.1.A, 7uxz.1.B, 7uxz.2.A, 7uxz.2.B, 7uxz.3.A, 7uxz.3.B, 7vbd.1.A, 7vbd.2.A, 7vbd.3.A, 7vbd.4.A, 7vbe.1.A, 7vbe.1.B, 7vbf.1.A, 7vbf.1.B, 7vnu.1.A, 7vnu.2.A, 7vnu.3.A, 7vnu.4.A, 7wzo.1.A, 7xwx.1.A, 7xwx.1.B, 7xwx.2.A, 7xwx.2.B, 7xwx.3.A, 7xwx.3.B, 7xwx.4.A, 7xwx.4.B, 7xwz.1.A, 7xwz.2.A, 7xx1.1.A, 7xx1.1.B, 7xx1.1.C, 7xx1.1.D, 7xxk.1.A, 7xxk.1.B, 7xxk.2.A, 7xxk.2.B, 7xxk.3.A, 7xxk.3.B