SWISS-MODEL Homology Modelling Report

Model Building Report

This document lists the results for the homology modelling project "Nucleoprotein (N) | P0DTC9" 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 299 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
0.23 0.68 ± 0.07
Template Seq Identity Oligo-state QSQE Found by Method Resolution Seq Similarity Range Coverage Description
4ud1.1.A 55.41 monomer 0.00 BLAST X-ray 2.48Å 0.47 40 - 174 0.37 N PROTEIN

Excluded ligands

Ligand Name.Number Reason for Exclusion Description
NH4.1 Not biologically relevant.
AMMONIUM ION

Target    MSDNGPQNQRNAPR-ITFGGPSDSTGSNQNGERSGARSKQRRPQGLPNNTASWFTALTQHGKEDLKFPRGQGVPINTNSS
4ud1.1.A -----------APRAVSFADNNDITNTNL----SRGRGRNPKPRAAPNNTVSWYTGLTQHGKVPLTFPPGQGVPLNANST

Target PDDQIGYYRRATRRIRGGDGKMKDLSPRWYFYYLGTGPEAGLPYGANKDGIIWVATEGALNTPKDHIGTRNPANNAAIVL
4ud1.1.A PAQNAGYWRRQDRKINTGNG-IKQLAPRWYFYYTGTGPEAALPFRAVKDGIVWVHEDGATDAPST-FGTRNPNNDSAIVT

Target QLPQGTTLPKGFYAEGSRGGSQASSRSSSRSRNSSRNSTPGSSRGTSPARMAGNGGDAALALLLLDRLNQLESKMSGKGQ
4ud1.1.A QFAPGTKLPKNFHIE-----------------------------------------------------------------

Target QQQGQTVTKKSAAEASKKPRQKRTATKAYNVTQAFGRRGPEQTQGNFGDQELIRQGTDYKHWPQIAQFAPSASAFFGMSR
4ud1.1.A --------------------------------------------------------------------------------

Target IGMEVTPSGTWLTYTGAIKLDDKDPNFKDQVILLNKHIDAYKTFPPTEPKKDKKKKADETQALPQRQKKQQTVTLLPAAD
4ud1.1.A --------------------------------------------------------------------------------

Target LDDFSKQLQQSMSSADSTQA
4ud1.1.A --------------------




Model #01

File Built with Oligo-State Ligands GMQE QMEANDisCo Global
PDB ProMod3 3.3.0 monomer
None
0.21 0.74 ± 0.07
Template Seq Identity Oligo-state QSQE Found by Method Resolution Seq Similarity Range Coverage Description
2ofz.1.A 92.06 monomer 0.00 HHblits X-ray 1.17Å 0.61 48 - 173 0.30 Nucleocapsid protein

Excluded ligands

Ligand Name.Number Reason for Exclusion Description
EDO.1 Not biologically relevant.
1,2-ETHANEDIOL

Target    MSDNGPQNQRNAPRITFGGPSDSTGSNQNGERSGARSKQRRPQGLPNNTASWFTALTQHGKEDLKFPRGQGVPINTNSSP
2ofz.1.A -----------------------------------------------NTASWFTALTQHGKEELRFPRGQGVPINTNSGP

Target DDQIGYYRRATRRIRGGDGKMKDLSPRWYFYYLGTGPEAGLPYGANKDGIIWVATEGALNTPKDHIGTRNPANNAAIVLQ
2ofz.1.A DDQIGYYRRATRRVRGGDGKMKELSPRWYFYYLGTGPEASLPYGANKEGIVWVATEGALNTPKDHIGTRNPNNNAATVLQ

Target LPQGTTLPKGFYAEGSRGGSQASSRSSSRSRNSSRNSTPGSSRGTSPARMAGNGGDAALALLLLDRLNQLESKMSGKGQQ
2ofz.1.A LPQGTTLPKGFYA-------------------------------------------------------------------

Target QQGQTVTKKSAAEASKKPRQKRTATKAYNVTQAFGRRGPEQTQGNFGDQELIRQGTDYKHWPQIAQFAPSASAFFGMSRI
2ofz.1.A --------------------------------------------------------------------------------

Target GMEVTPSGTWLTYTGAIKLDDKDPNFKDQVILLNKHIDAYKTFPPTEPKKDKKKKADETQALPQRQKKQQTVTLLPAADL
2ofz.1.A --------------------------------------------------------------------------------

Target DDFSKQLQQSMSSADSTQA
2ofz.1.A -------------------




Model #03

File Built with Oligo-State Ligands GMQE QMEANDisCo Global
PDB ProMod3 3.3.0 monomer (matching prediction)
None
0.18 0.60 ± 0.08
Template Seq Identity Oligo-state QSQE Found by Method Resolution Seq Similarity Range Coverage Description
6wzq.2.B 100.00 homo-dimer 0.49 HHblits X-ray 1.45Å 0.62 250 - 364 0.28 Nucleoprotein

Excluded ligands

Ligand Name.Number Reason for Exclusion Description
SO4.1 Not biologically relevant.
SULFATE ION
SO4.2 Not biologically relevant.
SULFATE ION
SO4.3 Not in contact with model.
SULFATE ION

Target    MSDNGPQNQRNAPRITFGGPSDSTGSNQNGERSGARSKQRRPQGLPNNTASWFTALTQHGKEDLKFPRGQGVPINTNSSP
6wzq.2.B --------------------------------------------------------------------------------

Target DDQIGYYRRATRRIRGGDGKMKDLSPRWYFYYLGTGPEAGLPYGANKDGIIWVATEGALNTPKDHIGTRNPANNAAIVLQ
6wzq.2.B --------------------------------------------------------------------------------

Target LPQGTTLPKGFYAEGSRGGSQASSRSSSRSRNSSRNSTPGSSRGTSPARMAGNGGDAALALLLLDRLNQLESKMSGKGQQ
6wzq.2.B --------------------------------------------------------------------------------

Target QQGQTVTKKSAAEASKKPRQKRTATKAYNVTQAFGRRGPEQTQGNFGDQELIRQGTDYKHWPQIAQFAPSASAFFGMSRI
6wzq.2.B ------TKKSAAEASKKPRQKRTATKAYNVTQAFGRRGPEQTQGNFGDQELIRQGTDYKHWPQIAQFAPSASAFFGMSRI

Target GMEVTPSGTWLTYTGAIKLDDKDPNFKDQVILLNKHIDAYKTFPPTEPKKDKKKKADETQALPQRQKKQQTVTLLPAADL
6wzq.2.B GMEVTPSGTWLTYTGAIKLDDKDPNFKDQVILLNKHIDAYKTFP------------------------------------

Target DDFSKQLQQSMSSADSTQA
6wzq.2.B -------------------




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.

MSDNGPQNQRNAPRITFGGPSDSTGSNQNGERSGARSKQRRPQGLPNNTASWFTALTQHGKEDLKFPRGQGVPINTNSSPDDQIGYYRRATRRIRGGDGK
MKDLSPRWYFYYLGTGPEAGLPYGANKDGIIWVATEGALNTPKDHIGTRNPANNAAIVLQLPQGTTLPKGFYAEGSRGGSQASSRSSSRSRNSSRNSTPG
SSRGTSPARMAGNGGDAALALLLLDRLNQLESKMSGKGQQQQGQTVTKKSAAEASKKPRQKRTATKAYNVTQAFGRRGPEQTQGNFGDQELIRQGTDYKH
WPQIAQFAPSASAFFGMSRIGMEVTPSGTWLTYTGAIKLDDKDPNFKDQVILLNKHIDAYKTFPPTEPKKDKKKKADETQALPQRQKKQQTVTLLPAADL
DDFSKQLQQSMSSADSTQA

Table T2:

Template Seq Identity Oligo-state QSQE Found by Method Resolution Seq Similarity Coverage Description
8fd5.1.A 100.00 monomer - HHblits EM NA 0.62 1.00 Nucleoprotein
4ud1.1.A 55.41 monomer - BLAST X-ray 2.48Å 0.47 0.37 N PROTEIN
7acs.1.A 100.00 monomer - HHblits NMR NA 0.63 0.33 Nucleoprotein
7sd4.1.A 100.00 monomer - HHblits NMR NA 0.63 0.32 Nucleoprotein
1ssk.1.A 92.70 monomer - HHblits NMR NA 0.61 0.33 Nucleocapsid protein
6m3m.2.A 100.00 monomer - HHblits X-ray 2.70Å 0.63 0.32 Nucleoprotein
6yi3.1.A 100.00 monomer - HHblits NMR NA 0.63 0.33 Nucleoprotein
1ssk.1.A 92.37 monomer - BLAST NMR NA 0.61 0.31 Nucleocapsid protein
7act.1.A 100.00 monomer - HHblits NMR NA 0.63 0.33 Nucleoprotein
6m3m.1.A 100.00 monomer - HHblits X-ray 2.70Å 0.63 0.32 Nucleoprotein
7cr5.1.A 100.00 monomer - HHblits X-ray 2.08Å 0.63 0.32 Nucleoprotein
2ofz.1.A 92.06 monomer - BLAST X-ray 1.17Å 0.61 0.30 Nucleocapsid protein
2ofz.1.A 92.06 monomer - HHblits X-ray 1.17Å 0.61 0.30 Nucleocapsid protein
6wzq.2.B 100.00 homo-dimer 0.49 HHblits X-ray 1.45Å 0.62 0.28 Nucleoprotein

The table above shows the top 14 filtered templates. A further 193 templates were found which were considered to be less suitable for modelling than the filtered list.
2btl.1.A, 2btl.2.A, 2bxx.1.A, 2c86.1.A, 2ca1.1.A, 2ca1.1.B, 2cjr.1.A, 2cjr.1.B, 2cjr.2.A, 2cjr.2.B, 2cjr.3.A, 2cjr.3.B, 2cjr.4.A, 2cjr.4.B, 2ge7.1.A, 2ge8.1.A, 2ge8.1.B, 2ge8.2.B, 2gec.1.A, 2gec.1.B, 2gib.1.A, 2jw8.1.A, 2jw8.1.B, 3hd4.1.A, 4j3k.1.A, 4kxj.1.A, 4lm9.1.A, 4lmc.1.A, 4ud1.1.A, 5epw.1.A, 5n4k.1.A, 6ff4.1.T, 6g13.1.A, 6g13.1.B, 6kl2.1.A, 6kl2.1.B, 6kl2.2.A, 6kl5.1.A, 6kl5.2.A, 6kl5.2.B, 6kl6.1.B, 6lnn.1.A, 6lnn.1.B, 6lz6.2.A, 6lz8.2.A, 6m3m.1.A, 6m3m.2.A, 6m3m.3.A, 6m3m.4.A, 6utc.1.A, 6vyo.1.A, 6vyo.1.B, 6vyo.1.C, 6vyo.1.D, 6wji.1.A, 6wji.1.B, 6wji.2.A, 6wji.2.B, 6wji.3.A, 6wji.3.B, 6wkp.1.A, 6wkp.1.B, 6wkp.1.C, 6wkp.1.D, 6wzo.1.A, 6wzo.1.B, 6wzo.2.A, 6wzo.2.B, 6wzq.1.A, 6wzq.1.B, 6wzq.2.A, 6wzq.2.B, 6yi3.1.A, 6yun.1.A, 6yun.1.B, 6zco.1.A, 6zco.1.B, 7abh.1.N, 7acs.1.A, 7act.1.A, 7c22.1.A, 7c22.1.B, 7c22.2.A, 7c22.2.B, 7cdz.1.A, 7cdz.2.A, 7cdz.3.A, 7cdz.4.A, 7ce0.1.A, 7ce0.1.B, 7ce0.2.A, 7ce0.2.B, 7de1.1.A, 7de1.1.B, 7dvq.1.j, 7dyd.1.B, 7dyd.2.B, 7f2b.1.A, 7f2b.1.B, 7f2e.1.A, 7f2e.1.B, 7f2e.2.A, 7f2e.2.B, 7f2e.3.A, 7f2e.3.B, 7f2e.4.A, 7f2e.4.B, 7f2e.5.A, 7f2e.5.B, 7f2e.6.A, 7f2e.6.B, 7n0i.1.A, 7n0i.1.B, 7n0i.2.A, 7n0i.2.B, 7n0i.3.A, 7n0i.3.B, 7n0i.4.A, 7n0i.4.C, 7n0r.1.A, 7n0r.2.A, 7n3c.1.C, 7n3d.1.C, 7n45.1.A, 7nn6.1.A, 7o05.1.A, 7o05.1.B, 7o05.2.A, 7o05.2.B, 7o35.1.A, 7o35.1.B, 7o35.2.A, 7o35.2.B, 7o36.1.A, 7o36.1.B, 7o36.2.A, 7o36.2.B, 7pku.1.B, 7r98.1.A, 7r98.2.A, 7r98.3.A, 7str.1.C, 7sts.1.C, 7sts.2.A, 7sue.1.C, 7sue.2.C, 7sue.3.C, 7sue.4.C, 7uxx.1.A, 7uxx.1.B, 7uxx.2.A, 7uxx.2.B, 7uxx.3.A, 7uxx.3.B, 7uxz.1.A, 7uxz.1.B, 7uxz.2.A, 7uxz.2.B, 7uxz.3.A, 7uxz.3.B, 7vbd.1.A, 7vbd.2.A, 7vbd.3.A, 7vbd.4.A, 7vbe.1.A, 7vbe.1.B, 7vbf.1.A, 7vbf.1.B, 7vnu.1.A, 7vnu.2.A, 7vnu.3.A, 7vnu.4.A, 7wzo.1.A, 7xwx.1.A, 7xwx.1.B, 7xwx.2.A, 7xwx.2.B, 7xwx.3.A, 7xwx.3.B, 7xwx.4.A, 7xwx.4.B, 7xwz.1.A, 7xwz.2.A, 7xx1.1.A, 7xx1.1.B, 7xx1.1.C, 7xx1.1.D, 7xxk.1.A, 7xxk.1.B, 7xxk.2.A, 7xxk.2.B, 7xxk.3.A, 7xxk.3.B