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:

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 model was built (see Materials and Methods "Model Building"):

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




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.

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