SWISS-MODEL Homology Modelling Report

Model Building Report

This document lists the results for the homology modelling project "nsp10 / nsp16 hetero-oligomeric complex | P0DTD1 PRO_0000449628, PRO_0000449633" 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 sequences in Table T1. For details on the template search, see Materials and Methods. Overall 43 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 hetero-1-1-mer
2 x BDF: beta-D-fructopyranose;
1 x SAM: S-ADENOSYLMETHIONINE;
2 x ZN: ZINC ION;
0.94 0.86 ± 0.05
Template Seq Identity Oligo-state QSQE Found by Method Resolution Seq Similarity Range Coverage Description
6w4h.1 100.00 hetero-1-1-mer - HHblits X-ray 1.80Å 0.63 A: 1-298 B: 18-133 1.00 2'-O-methyltransferase Non-structural protein 10

Included Ligands

Ligand Description
2 x BDF
beta-D-fructopyranose
1 x SAM
S-ADENOSYLMETHIONINE
2 x ZN
ZINC ION

Excluded ligands

Ligand Name.Number Reason for Exclusion Description
ACT.3 Not biologically relevant.
ACETATE ION
ACT.4 Not biologically relevant.
ACETATE ION
SO3.1 Not in contact with model.
SULFITE ION

Target    SSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAP
6w4h.1.A SSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAP

Target GTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFIQQK
6w4h.1.A GTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFIQQK

Target LALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLS
6w4h.1.A LALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLS

Target SYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN
6w4h.1.A SYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN

Target    AGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFGGASCCLYCRCH
6w4h.1.B AGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFGGASCCLYCRCH

Target IDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQ
6w4h.1.B IDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQ




Model #02

File Built with Oligo-State Ligands GMQE QMEANDisCo Global
PDB ProMod3 3.3.0 hetero-1-1-mer
1 x SAH: S-ADENOSYL-L-HOMOCYSTEINE;
2 x ZN: ZINC ION;
0.89 0.83 ± 0.05
Template Seq Identity Oligo-state QSQE Found by Method Resolution Seq Similarity Range Coverage Description
2xyq.1 95.13 hetero-1-1-mer 0.92 HHblits X-ray 2.00Å 0.61 A: 1-289 B: 10-131 0.94 PUTATIVE 2'-O-METHYL TRANSFERASE NON-STRUCTURAL PROTEIN 10

Included Ligands

Ligand Description
1 x SAH
S-ADENOSYL-L-HOMOCYSTEINE
2 x ZN
ZINC ION

Excluded ligands

Ligand Name.Number Reason for Exclusion Description
CL.1 Not in contact with model.
CHLORIDE ION
CL.2 Not biologically relevant.
CHLORIDE ION
MG.6 Not in contact with model.
MAGNESIUM ION
NA.4 Not in contact with model.
SODIUM ION
NA.5 Not biologically relevant.
SODIUM ION

Target    SSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAP
2xyq.1.A ASQAWQPGVAMPNLYKMQRMLLEKCDLQNYGENAVIPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAP

Target GTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFIQQK
2xyq.1.A GTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPRTKHVTKENDSKEGFFTYLCGFIKQK

Target LALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLS
2xyq.1.A LALGGSIAVKITEHSWNADLYKLMGHFSWWTAFVTNVNASSSEAFLIGANYLGKPKEQIDGYTMHANYIFWRNTNPIQLS

Target SYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN
2xyq.1.A SYSLFDMSKFPLKLRGTAVMSLKENQINDMIYSLLEKGRLIIRENNRVV---------

Target    AGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFGGASCCLYCRCH
2xyq.1.B ---------NSTVLSFCAFAVDPAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFGGASCCLYCRCH

Target IDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQ
2xyq.1.B IDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLRNTVCTVCGMWKGYGCSCD--------




Materials and Methods

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 sequences for which templates were searched and models were built.

AGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIP
TTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQ

SSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDL
NDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNAS
SSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN

Table T2:

Template Seq Identity Oligo-state QSQE Found by Method Resolution Seq Similarity Coverage Description
7jyy.1 100.00 hetero-1-1-mer 0.99 HHblits X-ray 2.05Å 0.63 1.00 2'-O-methyltransferase; Non-structural protein 10
8bzv.1 100.00 hetero-1-1-mer 0.99 HHblits X-ray 1.80Å 0.63 1.00 2'-O-methyltransferase nsp16; Non-structural protein 10
7l6t.1 100.00 hetero-1-1-mer 0.98 HHblits X-ray 1.78Å 0.63 1.00 2'-O-methyltransferase; Non-structural protein 10
3r24.1 94.39 hetero-1-1-mer 0.97 BLAST / HHblits X-ray 2.00Å 0.61 0.98 2'-O-methyl transferase; Non-structural protein 10 and Non-structural protein 11
2xyq.1 95.13 hetero-1-1-mer 0.92 HHblits X-ray 2.00Å 0.61 0.94 PUTATIVE 2'-O-METHYL TRANSFERASE; NON-STRUCTURAL PROTEIN 10

The table above shows the top 5 filtered templates. A further 37 templates were found which were considered to be less suitable for modelling than the filtered list.
2xyq.1, 5yn5.1, 6w4h.1, 6w61.1, 6w75.1, 6w75.2, 6wjt.1, 6wjt.2, 6wkq.1, 6wkq.2, 6wks.1, 6wq3.1, 6wrz.1, 6wvn.1, 6xkm.1, 6yz1.1, 7bq7.1, 7c2i.1, 7c2j.1, 7jhe.1, 7jib.1, 7jpe.1, 7jyy.2, 7jz0.1, 7jz0.2, 7koa.1, 7l6r.1, 7lw3.1, 7lw4.1, 7nh7.1, 7r1t.1, 7r1u.1, 7ult.1, 7ult.2, 8bsd.1, 8c5m.1, 8oto.1