SWISS-MODEL Homology Modelling Report

Model Building Report

This document lists the results for the homology modelling project "nsp7 / nsp8 hetero-oligomeric complex | P0DTD1 PRO_0000449625, PRO_0000449626" 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 138 templates were found (Table T2).

Models

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

Model #01

File Built with Oligo-State Ligands GMQE QMEANDisCo Global
PDB ProMod3 3.3.0 hetero-8-8-mer
None
0.90 0.74 ± 0.05
Template Seq Identity Oligo-state QSQE Found by Method Resolution Seq Similarity Range Coverage Description
2ahm.1 97.86 hetero-oligomer 0.67 HHblits X-ray 2.40Å 0.59 GEFHMNOP: 1-191 BACDIJKL: 1-74 1.00 Replicase polyprotein 1ab, heavy chain Replicase polyprotein 1ab, light chain

Excluded ligands

Ligand Name.Number Reason for Exclusion Description
GOL.2 Not biologically relevant.
GLYCEROL
GOL.3 Not biologically relevant.
GLYCEROL
GOL.4 Not biologically relevant.
GLYCEROL
GOL.5 Not biologically relevant.
GLYCEROL
GOL.6 Not biologically relevant.
GLYCEROL
GOL.8 Not biologically relevant.
GLYCEROL
GOL.9 Not biologically relevant.
GLYCEROL
GOL.10 Not biologically relevant.
GLYCEROL
GOL.11 Not biologically relevant.
GLYCEROL
GOL.12 Not biologically relevant.
GLYCEROL
SO4.1 Not biologically relevant.
SULFATE ION
SO4.7 Not biologically relevant.
SULFATE ION

Target    AIASEFSSLPSYAAFATAQEAYEQAVANGDSEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKR
2ahm.1.G AIASEFSSLPSYAAYATAQEAYEQAVANGDSEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKR

Target AKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVV
2ahm.1.G AKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVVPDYGTYKNTCDGNTFTYASALWEIQQVV

Target DADSKIVQLSEISMDNSPNLAWPLIVTALRANSAVKLQ
2ahm.1.G DADSKIVQLSEINMDNSPNLAWPLIVTALRANSAVKLQ


Target AIASEFSSLPSYAAFATAQEAYEQAVANGDSEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKR
2ahm.1.E AIASEFSSLPSYAAYATAQEAYEQAVANGDSEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKR

Target AKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVV
2ahm.1.E AKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVVPDYGTYKNTCDGNTFTYASALWEIQQVV

Target DADSKIVQLSEISMDNSPNLAWPLIVTALRANSAVKLQ
2ahm.1.E DADSKIVQLSEINMDNSPNLAWPLIVTALRANSAVKLQ


Target AIASEFSSLPSYAAFATAQEAYEQAVANGDSEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKR
2ahm.1.F AIASEFSSLPSYAAYATAQEAYEQAVANGDSEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKR

Target AKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVV
2ahm.1.F AKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVVPDYGTYKNTCDGNTFTYASALWEIQQVV

Target DADSKIVQLSEISMDNSPNLAWPLIVTALRANSAVKLQ
2ahm.1.F DADSKIVQLSEINMDNSPNLAWPLIVTALRANSAVKLQ


Target AIASEFSSLPSYAAFATAQEAYEQAVANGDSEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKR
2ahm.1.H AIASEFSSLPSYAAYATAQEAYEQAVANGDSEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKR

Target AKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVV
2ahm.1.H AKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVVPDYGTYKNTCDGNTFTYASALWEIQQVV

Target DADSKIVQLSEISMDNSPNLAWPLIVTALRANSAVKLQ
2ahm.1.H DADSKIVQLSEINMDNSPNLAWPLIVTALRANSAVKLQ


Target AIASEFSSLPSYAAFATAQEAYEQAVANGDSEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKR
2ahm.1.M AIASEFSSLPSYAAYATAQEAYEQAVANGDSEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKR

Target AKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVV
2ahm.1.M AKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVVPDYGTYKNTCDGNTFTYASALWEIQQVV

Target DADSKIVQLSEISMDNSPNLAWPLIVTALRANSAVKLQ
2ahm.1.M DADSKIVQLSEINMDNSPNLAWPLIVTALRANSAVKLQ


Target AIASEFSSLPSYAAFATAQEAYEQAVANGDSEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKR
2ahm.1.N AIASEFSSLPSYAAYATAQEAYEQAVANGDSEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKR

Target AKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVV
2ahm.1.N AKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVVPDYGTYKNTCDGNTFTYASALWEIQQVV

Target DADSKIVQLSEISMDNSPNLAWPLIVTALRANSAVKLQ
2ahm.1.N DADSKIVQLSEINMDNSPNLAWPLIVTALRANSAVKLQ


Target AIASEFSSLPSYAAFATAQEAYEQAVANGDSEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKR
2ahm.1.O AIASEFSSLPSYAAYATAQEAYEQAVANGDSEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKR

Target AKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVV
2ahm.1.O AKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVVPDYGTYKNTCDGNTFTYASALWEIQQVV

Target DADSKIVQLSEISMDNSPNLAWPLIVTALRANSAVKLQ
2ahm.1.O DADSKIVQLSEINMDNSPNLAWPLIVTALRANSAVKLQ


Target AIASEFSSLPSYAAFATAQEAYEQAVANGDSEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKR
2ahm.1.P AIASEFSSLPSYAAYATAQEAYEQAVANGDSEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKR

Target AKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVV
2ahm.1.P AKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVVPDYGTYKNTCDGNTFTYASALWEIQQVV

Target DADSKIVQLSEISMDNSPNLAWPLIVTALRANSAVKLQ
2ahm.1.P DADSKIVQLSEINMDNSPNLAWPLIVTALRANSAVKLQ

Target    SKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRA
2ahm.1.B SKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINRLCEEMLDNRA

Target TLQ
2ahm.1.B TLQ


Target SKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRA
2ahm.1.A SKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINRLCEEMLDNRA

Target TLQ
2ahm.1.A TLQ


Target SKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRA
2ahm.1.C SKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINRLCEEMLDNRA

Target TLQ
2ahm.1.C TLQ


Target SKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRA
2ahm.1.D SKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINRLCEEMLDNRA

Target TLQ
2ahm.1.D TLQ


Target SKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRA
2ahm.1.I SKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINRLCEEMLDNRA

Target TLQ
2ahm.1.I TLQ


Target SKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRA
2ahm.1.J SKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINRLCEEMLDNRA

Target TLQ
2ahm.1.J TLQ


Target SKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRA
2ahm.1.K SKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINRLCEEMLDNRA

Target TLQ
2ahm.1.K TLQ


Target SKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRA
2ahm.1.L SKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINRLCEEMLDNRA

Target TLQ
2ahm.1.L TLQ




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.

SKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQ

AIASEFSSLPSYAAFATAQEAYEQAVANGDSEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDN
DALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRANSAVKLQ

Table T2:

Template Seq Identity Oligo-state QSQE Found by Method Resolution Seq Similarity Coverage Description
2ahm.1 97.86 hetero-8-8-mer 0.67 HHblits X-ray 2.40Å 0.59 1.00 Replicase polyprotein 1ab, heavy chain; Replicase polyprotein 1ab, light chain
6xip.1 100.00 hetero-2-2-mer 0.63 HHblits X-ray 1.50Å 0.60 0.73 Non-structural protein 8; Non-structural protein 7
7bv1.1 100.00 hetero-1-2-mer 0.46 HHblits EM NA 0.60 1.00 Non-structural protein 8; Non-structural protein 7

The table above shows the top 3 filtered templates. A further 72 templates were found which were considered to be less suitable for modelling than the filtered list.
2ahm.1, 3ub0.1, 3ub0.2, 5f22.1, 6m5i.1, 6m71.1, 6nur.1, 6wiq.1, 6wqd.1, 6wtc.1, 6xez.1, 6xip.1, 6xqb.1, 6yhu.1, 6yhu.2, 6yyt.1, 7aap.1, 7b3b.1, 7b3c.1, 7b3d.1, 7btf.1, 7bv1.1, 7bv2.1, 7bw4.1, 7bzf.1, 7c2k.1, 7ctt.1, 7cxm.1, 7cxn.1, 7cyq.1, 7d4f.1, 7dcd.1, 7dcd.2, 7dcd.3, 7dcd.4, 7dfg.1, 7dfh.1, 7doi.1, 7dok.1, 7dte.1, 7ed5.1, 7egq.1, 7eiz.1, 7jlt.1, 7krn.1, 7kro.1, 7krp.1, 7l1f.1, 7oyg.1, 7ozu.1, 7ozv.1, 7rdx.1, 7rdy.1, 7rdz.1, 7re0.1, 7re1.1, 7re2.1, 7re3.1, 7thm.1, 7uo4.1, 7uo7.1, 7uo9.1, 7uob.1, 7uoe.1, 8g6r.1, 8gwb.1, 8gwe.1, 8gwf.1, 8gwg.1, 8gwi.1, 8gwn.1, 8gwo.1