|  | SWISS-MODEL Homology Modelling Report

## Model Building Report

This document lists the results for the homology modelling project "Proofreading exoribonuclease nsp14 (ExoN) | P0DTD1 PRO_0000449631" 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 90 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 | 2 x ZN: ZINC ION; | 0.87 | 0.82 ± 0.05

Template | Seq Identity | Oligo-state | QSQE | Found by | Method | Resolution | Seq Similarity | Range | Coverage | Description
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
5nfy.1.A | 94.88 | monomer | 0.00 | HHblits | X-ray | 3.38Å | 0.62 | 3 - 525 | 1.00 | Polyprotein 1ab

### Included Ligands

Ligand | Description
--- | ---
2 x ZN | ZINC ION

### Excluded ligands

Ligand Name.Number | Reason for Exclusion | Description
--- | --- | ---
PEG.4 | Not biologically relevant. | DI(HYDROXYETHYL)ETHER
PEG.5 | Not in contact with model. | DI(HYDROXYETHYL)ETHER
ZN.3 | Clashing with protein. | ZINC ION
ZN.6 | Binding site not conserved. | ZINC ION
ZN.7 | Binding site not conserved. | ZINC ION

    Target    AENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFITREEAI
    5nfy.1.A  AENVTGLFKDCSKIITGLHPTQAPTHLSVDIKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFITREEAI

    Target    RHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWN
    5nfy.1.A  RHVRAWIGFDVEGCHATRDAVGTNLPLQLGFSTGVNLVAVPTGYVDTENNTEFTRVNAKPPPGDQFKHLIPLMYKGLPWN

    Target    VVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPF
    5nfy.1.A  VVRIKIVQMLSDTLKGLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDKRATCFSTSSDTYACWNHSVGFDYVYNPF

    Target    MIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQHMVVKAA
    5nfy.1.A  MIDVQQWGFTGNLQSNHDQHCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWSVEYPIIGDELRVNSACRKVQHMVVKSA

    Target    LLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCR
    5nfy.1.A  LLADKFPVLHDIGNPKAIKCVPQAEVEWKFYDAQPCSDKAYKIEELFYSYAIHHDKFTDGVCLFWNCNVDRYPANAIVCR

    Target    FDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQVVSDIDYVPLKSATCITRCNLG
    5nfy.1.A  FDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKSAFTNLKQLPFFYYSDSPCESHGKQVVSDIDYVPLKSATCITRCNLG

    Target    GAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQ
    5nfy.1.A  GAVCRHHANEYRQYLDAYNMMISAGFSLWIYKQFDTYNLWNTFTRLQ

### Model #02 | File | Built with | Oligo-State | Ligands | GMQE | QMEANDisCo Global
--- | --- | --- | --- | --- | --- | ---
| PDB | ProMod3 3.3.0 | monomer | 1 x G3A: GUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE; 1 x MG: MAGNESIUM ION; 1 x SAH: S-ADENOSYL-L-HOMOCYSTEINE; 1 x ZN: ZINC ION; | 0.86 | 0.79 ± 0.05

Template | Seq Identity | Oligo-state | QSQE | Found by | Method | Resolution | Seq Similarity | Range | Coverage | Description
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
5c8s.1.B | 95.07 | monomer | 0.00 | HHblits | X-ray | 3.33Å | 0.62 | 1 - 525 | 1.00 | Guanine-N7 methyltransferase

### Included Ligands

Ligand | Description
--- | ---
1 x G3A | GUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE
1 x MG | MAGNESIUM ION
1 x SAH | S-ADENOSYL-L-HOMOCYSTEINE
1 x ZN | ZINC ION

### Excluded ligands

Ligand Name.Number | Reason for Exclusion | Description
--- | --- | ---
ZN.1 | Binding site not conserved. | ZINC ION
ZN.2 | Binding site not conserved. | ZINC ION
ZN.3 | Clashing with protein. | ZINC ION
ZN.5 | Clashing with protein. | ZINC ION

    Target    AENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFITREEAI
    5c8s.1.B  AENVTGLFKDCSKIITGLHPTQAPTHLSVDIKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFITREEAI

    Target    RHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWN
    5c8s.1.B  RHVRAWIGFDVEGCHATRDAVGTNLPLQLGFSTGVNLVAVPTGYVDTENNTEFTRVNAKPPPGDQFKHLIPLMYKGLPWN

    Target    VVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPF
    5c8s.1.B  VVRIKIVQMLSDTLKGLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDKRATCFSTSSDTYACWNHSVGFDYVYNPF

    Target    MIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQHMVVKAA
    5c8s.1.B  MIDVQQWGFTGNLQSNHDQHCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWSVEYPIIGDELRVNSACRKVQHMVVKSA

    Target    LLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCR
    5c8s.1.B  LLADKFPVLHDIGNPKAIKCVPQAEVEWKFYDAQPCSDKAYKIEELFYSYATHHDKFTDGVCLFWNCNVDRYPANAIVCR

    Target    FDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQVVSDIDYVPLKSATCITRCNLG
    5c8s.1.B  FDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKSAFTNLKQLPFFYYSDSPCESHGKQVVSDIDYVPLKSATCITRCNLG

    Target    GAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQ
    5c8s.1.B  GAVCRHHANEYRQYLDAYNMMISAGFSLWIYKQFDTYNLWNTFTRLQ

### Model #03 | File | Built with | Oligo-State | Ligands | GMQE | QMEANDisCo Global
--- | --- | --- | --- | --- | --- | ---
| PDB | ProMod3 3.3.0 | monomer | 1 x SAM: S-ADENOSYLMETHIONINE; 2 x ZN: ZINC ION; | 0.85 | 0.79 ± 0.05

Template | Seq Identity | Oligo-state | QSQE | Found by | Method | Resolution | Seq Similarity | Range | Coverage | Description
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
5c8t.1.B | 95.07 | monomer | 0.00 | HHblits | X-ray | 3.20Å | 0.62 | 1 - 525 | 1.00 | Guanine-N7 methyltransferase

### Included Ligands

Ligand | Description
--- | ---
1 x SAM | S-ADENOSYLMETHIONINE
2 x ZN | ZINC ION

### Excluded ligands

Ligand Name.Number | Reason for Exclusion | Description
--- | --- | ---
MG.6 | Not in contact with model. | MAGNESIUM ION
ZN.1 | Binding site not conserved. | ZINC ION
ZN.2 | Binding site not conserved. | ZINC ION
ZN.5 | Clashing with protein. | ZINC ION

    Target    AENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFITREEAI
    5c8t.1.B  AENVTGLFKDCSKIITGLHPTQAPTHLSVDIKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFITREEAI

    Target    RHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWN
    5c8t.1.B  RHVRAWIGFDVEGCHATRDAVGTNLPLQLGFSTGVNLVAVPTGYVDTENNTEFTRVNAKPPPGDQFKHLIPLMYKGLPWN

    Target    VVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPF
    5c8t.1.B  VVRIKIVQMLSDTLKGLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDKRATCFSTSSDTYACWNHSVGFDYVYNPF

    Target    MIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQHMVVKAA
    5c8t.1.B  MIDVQQWGFTGNLQSNHDQHCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWSVEYPIIGDELRVNSACRKVQHMVVKSA

    Target    LLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCR
    5c8t.1.B  LLADKFPVLHDIGNPKAIKCVPQAEVEWKFYDAQPCSDKAYKIEELFYSYATHHDKFTDGVCLFWNCNVDRYPANAIVCR

    Target    FDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQVVSDIDYVPLKSATCITRCNLG
    5c8t.1.B  FDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKSAFTNLKQLPFFYYSDSPCESHGKQVVSDIDYVPLKSATCITRCNLG

    Target    GAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQ
    5c8t.1.B  GAVCRHHANEYRQYLDAYNMMISAGFSLWIYKQFDTYNLWNTFTRLQ

## 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.

AENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREA
VGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTSMKYFVK
IGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIG
DELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCR
FDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNM
MISAGFSLWVYKQFDTYNLWNTFTRLQ

## Table T2:

Template | Seq Identity | Oligo-state | QSQE | Found by | Method | Resolution | Seq Similarity | Coverage | Description
--- | --- | --- | --- | --- | --- | --- | --- | --- | ---
7n0d.1.H | 99.81 | homo-tetramer | 0.51 | HHblits | EM | NA | 0.63 | 1.00 | Proofreading exoribonuclease
7n0d.1.B | 99.81 | homo-tetramer | 0.51 | HHblits | EM | NA | 0.63 | 1.00 | Proofreading exoribonuclease
7n0d.1.D | 99.81 | homo-tetramer | 0.51 | HHblits | EM | NA | 0.63 | 1.00 | Proofreading exoribonuclease
5nfy.4.A | 94.88 | monomer | - | HHblits | X-ray | 3.38Å | 0.62 | 1.00 | Polyprotein 1ab
5nfy.2.A | 94.88 | monomer | - | HHblits | X-ray | 3.38Å | 0.62 | 1.00 | Polyprotein 1ab
5nfy.1.A | 94.88 | monomer | - | HHblits | X-ray | 3.38Å | 0.62 | 1.00 | Polyprotein 1ab
5nfy.3.A | 94.88 | monomer | - | HHblits | X-ray | 3.38Å | 0.62 | 1.00 | Polyprotein 1ab
7n0c.1.B | 99.81 | monomer | - | HHblits | EM | NA | 0.63 | 1.00 | Proofreading exoribonuclease
5c8s.1.B | 95.07 | monomer | - | HHblits | X-ray | 3.33Å | 0.62 | 1.00 | Guanine-N7 methyltransferase
5c8t.1.B | 95.07 | monomer | - | HHblits | X-ray | 3.20Å | 0.62 | 1.00 | Guanine-N7 methyltransferase
7n0b.1.B | 100.00 | monomer | - | HHblits | EM | NA | 0.63 | 1.00 | Proofreading exoribonuclease
7egq.1.H | 100.00 | monomer | - | HHblits | EM | NA | 0.63 | 1.00 | Proofreading exoribonuclease
7egq.1.P | 100.00 | monomer | - | HHblits | EM | NA | 0.63 | 1.00 | Proofreading exoribonuclease
7eiz.1.I | 100.00 | monomer | - | HHblits | EM | NA | 0.63 | 1.00 | Proofreading exoribonuclease
7tw7.1.A | 90.20 | monomer | - | HHblits | X-ray | 1.62Å | 0.59 | 0.48 | Transcription factor ETV6,Proofreading exoribonuclease nsp14 chimera
7tw8.1.A | 90.20 | monomer | - | HHblits | X-ray | 1.55Å | 0.59 | 0.48 | Transcription factor ETV6,Proofreading exoribonuclease nsp14 chimera
7tw9.1.A | 90.20 | monomer | - | HHblits | X-ray | 1.41Å | 0.59 | 0.48 | Transcription factor ETV6,Proofreading exoribonuclease nsp14 chimera

The table above shows the top 17 filtered templates. A further 72 templates were found which were considered to be less suitable for modelling than the filtered list.
5c8s.2.B, 5c8t.2.B, 5c8u.2.B, 5skw.1.A, 5skx.1.A, 5sky.1.A, 5skz.1.A, 5sl0.1.A, 5sl1.1.A, 5sl2.1.A, 5sl3.1.A, 5sl4.1.A, 5sl5.1.A, 5sl6.1.A, 5sl7.1.A, 5sl8.1.A, 5sl9.1.A, 5sla.1.A, 5slb.1.A, 5slc.1.A, 5sld.1.A, 5sle.1.A, 5slf.1.A, 5slg.1.A, 5slh.1.A, 5sli.1.A, 5slj.1.A, 5slk.1.A, 5sll.1.A, 5slm.1.A, 5sln.1.A, 5slo.1.A, 5slp.1.A, 5slq.1.A, 5slr.1.A, 5sls.1.A, 5slt.1.A, 5slu.1.A, 5slv.1.A, 5slw.1.A, 5slx.1.A, 5sly.1.A, 5slz.1.A, 5sm0.1.A, 5sm1.1.A, 5sm2.1.A, 5sm3.1.A, 5sm4.1.A, 5sm5.1.A, 5sm6.1.A, 5sm7.1.A, 5sm8.1.A, 5sm9.1.A, 5sma.1.A, 5smb.1.A, 5smc.1.A, 5smd.1.A, 5sme.1.A, 5smf.1.A, 5smg.1.A, 5smh.1.A, 5smi.1.A, 5smk.1.A, 7diy.1.B, 7mc5.1.A, 7mc6.1.A, 7n0d.1.J, 7qgi.1.A, 7qif.1.A, 7r2v.1.A, 7r2v.2.A, 7tw7.1.A