SWISS-MODEL Homology Modelling Report

Model Building Report

This document lists the results for the homology modelling project "ORF7a protein (ORF7a) | P0DTC7" 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:

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 37 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
None
0.49 0.70 ± 0.09
Template Seq Identity Oligo-state QSQE Found by Method Resolution Seq Similarity Range Coverage Description
1yo4.1.A 91.57 monomer 0.00 BLAST NMR - 0.60 16 - 98 0.69 Hypothetical protein X4

The template contained no ligands.


Target    MKIILFLALITLATCELYHYQECVRGTTVLLKEPCSSGTYEGNSPFHPLADNKFALTCFSTQFAFACPDGVKHVYQLRAR
1yo4.1.A ---------------ELYHYQECVRGTTVLLKEPCPSGTYEGNSPFHPLADNKFALTCTSTHFAFACADGTRHTYQLRAR

Target SVSPKLFIRQEEV-QELYSPIFLIVAAIVFITLCFTLKRKTE
1yo4.1.A SVSPKLFIRQEEVQQELYS-----------------------




Model #03

File Built with Oligo-State Ligands GMQE QMEANDisCo Global
PDB ProMod3 3.3.0 monomer
None
0.46 0.81 ± 0.11
Template Seq Identity Oligo-state QSQE Found by Method Resolution Seq Similarity Range Coverage Description
1xak.1.A 87.80 monomer 0.00 HHblits X-ray 1.80Å 0.59 15 - 82 0.68 SARS ORF7A ACCESSORY PROTEIN

The template contained no ligands.


Target    MKIILFLALITLATCELYHYQECVRGTTVLLKEPCSSGTYEGNSPFHPLADNKFALTCFSTQFAFACPDGVKHVYQLRAR
1xak.1.A -------------SCELYHYQECVRGTTVILKEPCPSGTYEGNSPFHPLADNKFALTCTSTHFAFACADGTRHTYQLRAR

Target SVSPKLFIRQEEVQELYSPIFLIVAAIVFITLCFTLKRKTE
1xak.1.A SVSPKLFIRQEEVQQ--------------------------




Model #02

File Built with Oligo-State Ligands GMQE QMEANDisCo Global
PDB ProMod3 3.3.0 monomer
None
0.40 0.80 ± 0.11
Template Seq Identity Oligo-state QSQE Found by Method Resolution Seq Similarity Range Coverage Description
6w37.1.A 100.00 monomer 0.00 HHblits X-ray 2.90Å 0.63 16 - 81 0.55 ORF7a protein

The template contained no ligands.


Target    MKIILFLALITLATCELYHYQECVRGTTVLLKEPCSSGTYEGNSPFHPLADNKFALTCFSTQFAFACPDGVKHVYQLRAR
6w37.1.A ---------------ELYHYQECVRGTTVLLKEPCSSGTYEGNSPFHPLADNKFALTCFSTQFAFACPDGVKHVYQLRAR

Target SVSPKLFIRQEEVQELYSPIFLIVAAIVFITLCFTLKRKTE
6w37.1.A SV---------------------------------------




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.

MKIILFLALITLATCELYHYQECVRGTTVLLKEPCSSGTYEGNSPFHPLADNKFALTCFSTQFAFACPDGVKHVYQLRARSVSPKLFIRQEEVQELYSPI
FLIVAAIVFITLCFTLKRKTE

Table T2:

Template Seq Identity Oligo-state QSQE Found by Method Resolution Seq Similarity Coverage Description
1yo4.1.A 91.57 monomer - HHblits NMR NA 0.60 0.69 Hypothetical protein X4
1yo4.1.A 91.57 monomer - BLAST NMR NA 0.60 0.69 Hypothetical protein X4
7ci3.1.A 100.00 monomer - HHblits X-ray 2.20Å 0.63 0.69 Orf7a protein
7ci3.1.A 100.00 monomer - BLAST X-ray 2.20Å 0.63 0.68 Orf7a protein
1xak.1.A 87.80 monomer - HHblits X-ray 1.80Å 0.59 0.68 SARS ORF7A ACCESSORY PROTEIN
1xak.1.A 88.89 monomer - BLAST X-ray 1.80Å 0.60 0.67 SARS ORF7A ACCESSORY PROTEIN
6w37.1.A 100.00 monomer - HHblits X-ray 2.90Å 0.63 0.55 ORF7a protein
7kuy.1.C 7.32 monomer - HHblits EM NA 0.25 0.34 Glycine receptor subunit alpha-2
7kuy.1.A 7.32 monomer - HHblits EM NA 0.25 0.34 Glycine receptor subunit alpha-2
7kuy.1.B 7.32 monomer - HHblits EM NA 0.25 0.34 Glycine receptor subunit alpha-2
5bkf.1.A 7.32 monomer - HHblits EM NA 0.25 0.34 Glycine receptor subunit alpha-2
5bkg.1.B 7.32 monomer - HHblits EM NA 0.25 0.34 Glycine receptor subunit alpha-2
5bkg.1.A 7.32 monomer - HHblits EM NA 0.25 0.34 Glycine receptor subunit alpha-2
5bkg.1.D 7.32 monomer - HHblits EM NA 0.25 0.34 Glycine receptor subunit alpha-2
5bkg.1.C 7.32 monomer - HHblits EM NA 0.25 0.34 Glycine receptor subunit alpha-2

The table above shows the top 15 filtered templates. A further 22 templates were found which were considered to be less suitable for modelling than the filtered list.
3jad.1.A, 3jae.1.A, 5cfb.1.B, 5tio.1.E, 5vdi.1.A, 5yje.1.A, 5yje.1.B, 5yje.1.C, 6vq6.1.U, 6xbw.1.U, 7f8l.1.A, 7f8l.1.B, 7khr.1.U, 7kuy.1.D, 7l31.1.A, 7l31.1.B, 7l31.1.C, 7l31.1.D, 7mx9.1.A, 7mx9.1.B, 7u8o.1.W, 7u8p.1.V