SWISS-MODEL Homology Modelling Report

Model Building Report

This document lists the results for the homology modelling project "Host translation inhibitor nsp1 | P0DTD1 PRO_0000449619" 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:

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 38 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
0.54 0.76 ± 0.08
Template Seq Identity Oligo-state QSQE Found by Method Resolution Seq Similarity Range Coverage Description
7k7p.1.A 100.00 monomer 0.00 HHblits X-ray 1.77Å 0.61 10 - 126 0.66 Host translation inhibitor nsp1

The template contained no ligands.


Target    MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRSDARTAP
7k7p.1.A ---------EKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRSDARTAP

Target HGHVMVELVAELEGIQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQEN
7k7p.1.A HGHVMVELVAELEGIQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNG---------------------------------

Target WNTKHSSGVTRELMRELNGG
7k7p.1.A --------------------




Model #01

File Built with Oligo-State Ligands GMQE QMEANDisCo Global
PDB ProMod3 3.3.0 monomer
None
0.24 0.67 ± 0.12
Template Seq Identity Oligo-state QSQE Found by Method Resolution Seq Similarity Range Coverage Description
6zoj.1.8 100.00 monomer 0.00 HHblits EM - 0.61 148 - 180 1.00 Non-structural protein 1

Excluded ligands

Ligand Name.Number Reason for Exclusion Description
MG.1 Not biologically relevant.
MAGNESIUM ION
MG.2 Not biologically relevant.
MAGNESIUM ION
MG.3 Not biologically relevant.
MAGNESIUM ION
MG.4 Not biologically relevant.
MAGNESIUM ION
MG.5 Not biologically relevant.
MAGNESIUM ION
MG.6 Not biologically relevant.
MAGNESIUM ION
MG.7 Not in contact with model.
MAGNESIUM ION
MG.8 Not biologically relevant.
MAGNESIUM ION
MG.9 Not biologically relevant.
MAGNESIUM ION
MG.10 Not biologically relevant.
MAGNESIUM ION
MG.11 Not in contact with model.
MAGNESIUM ION
MG.12 Binding site not conserved.
MAGNESIUM ION
MG.13 Not biologically relevant.
MAGNESIUM ION
MG.14 Not biologically relevant.
MAGNESIUM ION
MG.15 Not biologically relevant.
MAGNESIUM ION
MG.16 Not biologically relevant.
MAGNESIUM ION
MG.17 Not biologically relevant.
MAGNESIUM ION
MG.18 Binding site not conserved.
MAGNESIUM ION
MG.19 Not biologically relevant.
MAGNESIUM ION
MG.20 Not in contact with model.
MAGNESIUM ION
MG.21 Not biologically relevant.
MAGNESIUM ION
MG.22 Not biologically relevant.
MAGNESIUM ION
MG.23 Binding site not conserved.
MAGNESIUM ION
MG.24 Not biologically relevant.
MAGNESIUM ION
MG.25 Not biologically relevant.
MAGNESIUM ION
MG.26 Not biologically relevant.
MAGNESIUM ION
MG.27 Not biologically relevant.
MAGNESIUM ION
MG.28 Not in contact with model.
MAGNESIUM ION
MG.29 Not biologically relevant.
MAGNESIUM ION
MG.30 Not biologically relevant.
MAGNESIUM ION
MG.31 Not biologically relevant.
MAGNESIUM ION
MG.32 Not biologically relevant.
MAGNESIUM ION
MG.33 Not in contact with model.
MAGNESIUM ION
MG.34 Binding site not conserved.
MAGNESIUM ION
MG.35 Not biologically relevant.
MAGNESIUM ION
MG.36 Not biologically relevant.
MAGNESIUM ION
MG.37 Not biologically relevant.
MAGNESIUM ION
MG.38 Not biologically relevant.
MAGNESIUM ION
MG.39 Not in contact with model.
MAGNESIUM ION
MG.40 Not biologically relevant.
MAGNESIUM ION
MG.41 Not biologically relevant.
MAGNESIUM ION
MG.42 Not biologically relevant.
MAGNESIUM ION
MG.43 Not biologically relevant.
MAGNESIUM ION
MG.44 Not biologically relevant.
MAGNESIUM ION
MG.45 Binding site not conserved.
MAGNESIUM ION
MG.46 Not biologically relevant.
MAGNESIUM ION
MG.47 Not biologically relevant.
MAGNESIUM ION
MG.48 Not biologically relevant.
MAGNESIUM ION
MG.49 Not biologically relevant.
MAGNESIUM ION
MG.50 Not biologically relevant.
MAGNESIUM ION
MG.51 Not biologically relevant.
MAGNESIUM ION
MG.52 Binding site not conserved.
MAGNESIUM ION
MG.53 Not biologically relevant.
MAGNESIUM ION
MG.54 Not biologically relevant.
MAGNESIUM ION
MG.55 Not biologically relevant.
MAGNESIUM ION
MG.56 Not biologically relevant.
MAGNESIUM ION
MG.57 Not biologically relevant.
MAGNESIUM ION
MG.58 Binding site not conserved.
MAGNESIUM ION
MG.59 Not in contact with model.
MAGNESIUM ION
MG.60 Not biologically relevant.
MAGNESIUM ION
MG.61 Not biologically relevant.
MAGNESIUM ION
MG.62 Not in contact with model.
MAGNESIUM ION
MG.63 Not in contact with model.
MAGNESIUM ION
MG.64 Not in contact with model.
MAGNESIUM ION
MG.65 Not biologically relevant.
MAGNESIUM ION
MG.66 Not in contact with model.
MAGNESIUM ION
MG.67 Not biologically relevant.
MAGNESIUM ION
MG.68 Not in contact with model.
MAGNESIUM ION
MG.69 Not biologically relevant.
MAGNESIUM ION
MG.70 Not biologically relevant.
MAGNESIUM ION
MG.71 Not biologically relevant.
MAGNESIUM ION
MG.72 Not biologically relevant.
MAGNESIUM ION
MG.73 Not biologically relevant.
MAGNESIUM ION
MG.74 Not biologically relevant.
MAGNESIUM ION
MG.75 Not biologically relevant.
MAGNESIUM ION
MG.76 Not in contact with model.
MAGNESIUM ION
MG.77 Not biologically relevant.
MAGNESIUM ION
MG.78 Not biologically relevant.
MAGNESIUM ION
MG.79 Not in contact with model.
MAGNESIUM ION
MG.80 Not in contact with model.
MAGNESIUM ION
MG.81 Not biologically relevant.
MAGNESIUM ION
MG.82 Not in contact with model.
MAGNESIUM ION
MG.83 Not in contact with model.
MAGNESIUM ION
MG.84 Not biologically relevant.
MAGNESIUM ION
MG.85 Not in contact with model.
MAGNESIUM ION
MG.86 Not in contact with model.
MAGNESIUM ION
MG.87 Not biologically relevant.
MAGNESIUM ION
MG.88 Not in contact with model.
MAGNESIUM ION
MG.89 Not in contact with model.
MAGNESIUM ION
MG.90 Not biologically relevant.
MAGNESIUM ION
MG.91 Not biologically relevant.
MAGNESIUM ION
MG.92 Not in contact with model.
MAGNESIUM ION
MG.93 Binding site not conserved.
MAGNESIUM ION
MG.94 Not in contact with model.
MAGNESIUM ION
MG.95 Not in contact with model.
MAGNESIUM ION
MG.96 Not biologically relevant.
MAGNESIUM ION
MG.97 Binding site not conserved.
MAGNESIUM ION
MG.98 Not biologically relevant.
MAGNESIUM ION
MG.99 Not biologically relevant.
MAGNESIUM ION
MG.100 Not biologically relevant.
MAGNESIUM ION
MG.101 Not biologically relevant.
MAGNESIUM ION
MG.102 Not biologically relevant.
MAGNESIUM ION
MG.103 Not biologically relevant.
MAGNESIUM ION
MG.104 Not in contact with model.
MAGNESIUM ION
MG.105 Not in contact with model.
MAGNESIUM ION
MG.106 Not biologically relevant.
MAGNESIUM ION
MG.107 Not biologically relevant.
MAGNESIUM ION
MG.108 Not biologically relevant.
MAGNESIUM ION
MG.109 Not biologically relevant.
MAGNESIUM ION
MG.110 Not biologically relevant.
MAGNESIUM ION
MG.111 Not biologically relevant.
MAGNESIUM ION
MG.112 Not biologically relevant.
MAGNESIUM ION
MG.113 Binding site not conserved.
MAGNESIUM ION
MG.114 Not in contact with model.
MAGNESIUM ION
MG.115 Not biologically relevant.
MAGNESIUM ION
MG.116 Not biologically relevant.
MAGNESIUM ION
MG.117 Not in contact with model.
MAGNESIUM ION
MG.118 Not biologically relevant.
MAGNESIUM ION
MG.119 Not in contact with model.
MAGNESIUM ION
MG.120 Not in contact with model.
MAGNESIUM ION
MG.121 Not biologically relevant.
MAGNESIUM ION
MG.122 Not biologically relevant.
MAGNESIUM ION
MG.123 Not biologically relevant.
MAGNESIUM ION
MG.124 Not biologically relevant.
MAGNESIUM ION
MG.125 Not biologically relevant.
MAGNESIUM ION
MG.126 Not biologically relevant.
MAGNESIUM ION
MG.127 Not biologically relevant.
MAGNESIUM ION
MG.128 Not in contact with model.
MAGNESIUM ION
MG.129 Not in contact with model.
MAGNESIUM ION
MG.130 Binding site not conserved.
MAGNESIUM ION
MG.131 Not biologically relevant.
MAGNESIUM ION
MG.132 Not biologically relevant.
MAGNESIUM ION
MG.133 Not in contact with model.
MAGNESIUM ION
MG.134 Not biologically relevant.
MAGNESIUM ION
MG.135 Not biologically relevant.
MAGNESIUM ION
MG.136 Not biologically relevant.
MAGNESIUM ION
MG.137 Not in contact with model.
MAGNESIUM ION
MG.138 Not biologically relevant.
MAGNESIUM ION
MG.139 Not in contact with model.
MAGNESIUM ION
MG.140 Binding site not conserved.
MAGNESIUM ION
MG.141 Binding site not conserved.
MAGNESIUM ION
MG.142 Not biologically relevant.
MAGNESIUM ION
MG.143 Binding site not conserved.
MAGNESIUM ION
MG.144 Binding site not conserved.
MAGNESIUM ION
MG.145 Not biologically relevant.
MAGNESIUM ION
MG.146 Not biologically relevant.
MAGNESIUM ION
MG.147 Not biologically relevant.
MAGNESIUM ION
MG.148 Not biologically relevant.
MAGNESIUM ION
MG.149 Not biologically relevant.
MAGNESIUM ION
MG.150 Not biologically relevant.
MAGNESIUM ION
MG.151 Not biologically relevant.
MAGNESIUM ION
MG.152 Not biologically relevant.
MAGNESIUM ION
MG.153 Not biologically relevant.
MAGNESIUM ION
MG.154 Not biologically relevant.
MAGNESIUM ION
MG.155 Not biologically relevant.
MAGNESIUM ION
MG.156 Binding site not conserved.
MAGNESIUM ION
MG.157 Not biologically relevant.
MAGNESIUM ION
MG.158 Not biologically relevant.
MAGNESIUM ION
MG.159 Not biologically relevant.
MAGNESIUM ION
MG.160 Binding site not conserved.
MAGNESIUM ION
MG.161 Binding site not conserved.
MAGNESIUM ION
MG.162 Binding site not conserved.
MAGNESIUM ION
MG.163 Binding site not conserved.
MAGNESIUM ION
MG.164 Binding site not conserved.
MAGNESIUM ION
MG.165 Binding site not conserved.
MAGNESIUM ION
MG.166 Binding site not conserved.
MAGNESIUM ION
ZN.167 Binding site not conserved.
ZINC ION
ZN.168 Binding site not conserved.
ZINC ION
ZN.169 Binding site not conserved.
ZINC ION

Target    MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRSDARTAP
6zoj.1.8 MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRSDARTAP

Target HGHVMVELVAELEGIQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQEN
6zoj.1.8 HGHVMVELVAELEGIQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQEN

Target WNTKHSSGVTRELMRELNGG
6zoj.1.8 WNTKHSSGVTRELMRELNGG




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

Table T1:

Primary amino acid sequence for which templates were searched and models were built.

MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRSDARTAPHGHVMVELVAELEGIQYGRS
GETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGG

Table T2:

Template Seq Identity Oligo-state QSQE Found by Method Resolution Seq Similarity Coverage Description
7k7p.1.A 100.00 monomer - HHblits X-ray 1.77Å 0.61 0.66 Host translation inhibitor nsp1
2gdt.1.A 86.09 monomer - BLAST NMR NA 0.56 0.64 Leader protein; p65 homolog; NSP1 (EC 3.4.22.-)
2gdt.1.A 83.33 monomer - HHblits NMR NA 0.55 0.63 Leader protein; p65 homolog; NSP1 (EC 3.4.22.-)
7opl.1.E 86.09 monomer - BLAST EM NA 0.56 0.64 Non-structural protein 1
7opl.1.E 84.07 monomer - HHblits EM NA 0.55 0.63 Non-structural protein 1
6zok.1.U 100.00 monomer - HHblits EM NA 0.61 1.00 Non-structural protein 1
6zp4.1.r 100.00 monomer - HHblits EM NA 0.61 1.00 Non-structural protein 1
6zoj.1.8 100.00 monomer - HHblits EM NA 0.61 1.00 Non-structural protein 1
6zlw.1.9 100.00 monomer - HHblits EM NA 0.61 1.00 Non-structural protein 1
6zmt.1.7 100.00 monomer - HHblits EM NA 0.61 1.00 Non-structural protein 1
6zon.1.l 100.00 monomer - HHblits EM NA 0.61 1.00 Host translation inhibitor Nsp1
6zm7.81.A 100.00 monomer - HHblits EM NA 0.61 1.00 Non-structural protein 1
6zn5.1.8 100.00 monomer - HHblits EM NA 0.61 1.00 Non-structural protein 1

The table above shows the top 13 filtered templates. A further 24 templates were found which were considered to be less suitable for modelling than the filtered list.
2gk4.1.A, 2gk4.1.B, 3w3a.2.H, 5gar.1.L, 5gas.1.L, 6jqy.1.A, 6jqy.1.B, 6zme.81.A, 6zmi.81.A, 6zmo.82.A, 7eq4.1.A, 7jqb.1.0, 7jqc.1.0, 7k3n.1.A, 7k5i.1.9, 7wuw.1.C, 8a4y.1.A, 8a55.1.A, 8aou.1.A, 8asq.1.A, 8ays.1.A, 8ayw.1.A, 8az8.1.A, 8az9.1.A