Model Building Report

This document lists the results for the homology modelling project "RNA-directed RNA polymerase nsp12 (Pol) | P0DTD1 PRO_0000449629" 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:

• Waterhouse A, Bertoni M, Bienert S, Studer G, Tauriello G, Gumienny R, Heer FT, de Beer TAP, Rempfer C, Bordoli L, Lepore R, Schwede T
  SWISS-MODEL: homology modelling of protein structures and complexes.
  Nucleic Acids Res 46, W296-W303. (2018) 2978835510.1093/nar/gky427
• Bienert S, Waterhouse A, de Beer TAP, Tauriello G, Studer G, Bordoli L, Schwede T
  The SWISS-MODEL Repository - new features and functionality.
  Nucleic Acids Res 45, D313-D319. (2017) 2789967210.1093/nar/gkw1132
• Studer G, Tauriello G, Bienert S, Biasini M, Johner N, Schwede T
  ProMod3 - A versatile homology modelling toolbox.
  PLOS Comp Biol 17(1), e1008667. (2021) 3350798010.1371/journal.pcbi.1008667
• Studer G, Rempfer C, Waterhouse AM, Gumienny R, Haas J, Schwede T
  QMEANDisCo - distance constraints applied on model quality estimation.
  Bioinformatics 36, 1765-1771. (2020) 3169731210.1093/bioinformatics/btz828
• Bertoni M, Kiefer F, Biasini M, Bordoli L, Schwede T
  Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology.
  Scientific Reports 7. (2017) 2887468910.1038/s41598-017-09654-8

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 349 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	monomer	2 x ZN: ZINC ION;	0.85	0.89 ± 0.05

Template	Seq Identity	Oligo-state	QSQE	Found by	Method	Resolution	Seq Similarity	Range	Coverage	Description
6nur.1.A	96.35	monomer	0.00	HHblits	EM	-	0.61	117 - 919	1.00	NSP12

Included Ligands

Ligand	Description
2 x ZN	ZINC ION

Target    SADAQSFLNRVCGVSAARLTPCGTGTSTDVVYRAFDIYNDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNY
6nur.1.A  SADASTFLNRVCGVSAARLTPCGTGTSTDVVYRAFDIYNEKVAGFAKFLKTNCCRFQEKDEEGNLLDSYFVVKRHTMSNY

Target    QHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKK
6nur.1.A  QHEETIYNLVKDCPAVAVHDFFKFRVDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKK

Target    DWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSL
6nur.1.A  DWYDFVENPDILRVYANLGERVRQSLLKTVQFCDAMRDAGIVGVLTLDNQDLNGNWYDFGDFVQVAPGCGVPIVDSYYSL

Target    LMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTV
6nur.1.A  LMPILTLTRALAAESHMDADLAKPLIKWDLLKYDFTEERLCLFDRYFKYWDQTYHPNCINCLDDRCILHCANFNVLFSTV

Target    FPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAA
6nur.1.A  FPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAA

Target    LTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYF
6nur.1.A  LTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYF

Target    DCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGV
6nur.1.A  DCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGV

Target    SICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLAR
6nur.1.A  SICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVETPHLMGWDYPKCDRAMPNMLRIMASLVLAR

Target    KHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYV
6nur.1.A  KHNTCCNLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYV

Target    RNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCW
6nur.1.A  RNLQHRLYECLYRNRDVDHEFVDEFYAYLRKHFSMMILSDDAVVCYNSNYAAQGLVASIKNFKAVLYYQNNVFMSEAKCW

Target    TETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADV
6nur.1.A  TETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADV

Target    FHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQ
6nur.1.A  FHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVL-

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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

• Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL
  BLAST+: architecture and applications.
  BMC Bioinformatics, 10, 421-430. (2009) 2000350010.1186/1471-2105-10-421
• Steinegger M, Meier M, Mirdita M, Vöhringer H, Haunsberger SJ, Söding J
  HH-suite3 for fast remote homology detection and deep protein annotation.
  BMC Bioinformatics 20, 473. (2019) 3152111010.1186/s12859-019-3019-7

Table T1:

Primary amino acid sequence for which templates were searched and models were built.

Table T2:

Template	Seq Identity	Oligo-state	QSQE	Found by	Method	Resolution	Seq Similarity	Coverage	Description
7re1.1.A	100.00	monomer	-	HHblits	EM	NA	0.63	1.00	RNA-directed RNA polymerase
7rdz.1.A	100.00	monomer	-	HHblits	EM	NA	0.63	1.00	RNA-directed RNA polymerase
7rdx.1.A	100.00	monomer	-	HHblits	EM	NA	0.63	1.00	RNA-directed RNA polymerase
7krp.1.A	100.00	monomer	-	HHblits	EM	NA	0.63	1.00	RNA-directed RNA polymerase
7re3.1.J	100.00	homo-dimer	0.71	HHblits	EM	NA	0.63	1.00	RNA-directed RNA polymerase
7krn.1.A	100.00	monomer	-	HHblits	EM	NA	0.63	1.00	RNA-directed RNA polymerase
7kro.1.A	100.00	monomer	-	HHblits	EM	NA	0.63	1.00	RNA-directed RNA polymerase
7aap.1.A	100.00	monomer	-	HHblits	EM	NA	0.63	1.00	Non-structural protein 12
6m71.1.A	100.00	monomer	-	HHblits	EM	NA	0.63	1.00	RNA-directed RNA polymerase
7bv2.1.A	100.00	monomer	-	HHblits	EM	NA	0.63	1.00	RNA-directed RNA polymerase
6nur.1.A	96.35	monomer	-	HHblits	EM	NA	0.61	1.00	NSP12

The table above shows the top 11 filtered templates. A further 336 templates were found which were considered to be less suitable for modelling than the filtered list.
1csj.1.A, 1gx6.1.A, 1khv.1.A, 1khv.2.A, 1nb7.1.A, 1nb7.2.A, 1nhu.1.A, 1raj.1.A, 1rdr.1.A, 1s48.1.A, 1s4f.1.A, 1s4f.2.A, 1s4f.3.A, 1s4f.4.A, 1sh0.1.A, 1sh2.1.A, 1sh3.1.A, 1sh3.2.A, 1tp7.1.A, 1tp7.3.A, 1tql.1.A, 1wne.1.A, 1xr5.1.A, 1xr6.1.A, 1xr7.1.A, 1yuy.1.A, 1yvf.1.A, 1yvx.1.A, 2awz.1.A, 2b43.1.A, 2cjq.1.A, 2ckw.1.A, 2d3z.1.A, 2dxs.1.A, 2f8e.1.A, 2fvc.1.A, 2gc8.1.A, 2giq.1.A, 2hai.1.A, 2ijd.1.A, 2ijd.2.A, 2ijf.1.A, 2ily.1.A, 2j7w.1.A, 2jc0.1.A, 2o5d.1.A, 2qe2.1.A, 2qe5.1.A, 2uut.1.A, 2uuw.1.A, 2wcx.1.A, 2who.1.A, 2wk4.1.A, 2wk4.1.B, 2wrm.1.A, 2xhu.1.A, 2xhv.1.A, 2xhw.1.A, 2xi2.1.A, 2xwh.1.A, 2xxd.1.A, 2xym.1.A, 2zku.1.A, 3cdu.1.A, 3cwj.1.A, 3ddk.1.A, 3fql.1.A, 3frz.1.A, 3gnv.1.A, 3gol.2.A, 3gsz.1.A, 3h5s.1.A, 3h5x.1.A, 3hhk.1.A, 3hkw.1.A, 3i5k.1.A, 3klv.1.A, 3kmq.1.A, 3kms.1.A, 3kna.1.A, 3koa.1.A, 3lkh.2.A, 3mf5.1.A, 3n6l.1.A, 3n6m.1.A, 3nai.1.A, 3nai.2.A, 3nai.2.B, 3nky.1.A, 3nl0.1.A, 3nma.1.A, 3ol8.4.A, 3qgd.1.A, 3qge.2.A, 3qgg.1.A, 3qgi.1.A, 3qid.1.A, 3qid.2.A, 3qid.2.B, 3sfg.1.A, 3sfg.2.A, 3sfg.2.B, 3sfu.1.A, 3sfu.2.A, 3sfu.2.B, 3ske.1.A, 3u4r.1.A, 3upf.1.A, 3upf.2.A, 3upi.1.A, 3uqs.1.A, 3ur0.4.E, 3vqs.1.A, 3vqs.2.A, 3vws.1.A, 4adp.1.A, 4aep.1.A, 4c11.1.A, 4c11.1.B, 4dru.1.A, 4e76.1.A, 4eaw.1.A, 4eo6.1.A, 4gmc.1.A, 4gmc.2.A, 4hdg.1.A, 4hhj.1.A, 4ika.1.A, 4iqx.1.A, 4j0a.2.A, 4k4s.1.A, 4k4u.1.A, 4k4w.1.A, 4k4x.1.A, 4k50.2.A, 4k6m.1.A, 4kai.1.A, 4kb7.1.A, 4khm.1.A, 4khr.1.A, 4lq3.1.A, 4lq9.1.A, 4mtp.1.A, 4mz4.2.A, 4nld.1.A, 4nlo.1.A, 4nlp.1.A, 4nlq.1.A, 4nlr.1.A, 4nls.1.A, 4nlt.1.A, 4nlu.1.A, 4nlv.1.A, 4nlw.1.A, 4nlx.1.A, 4nly.1.A, 4nru.1.A, 4nyz.1.A, 4nz0.1.A, 4nz0.2.A, 4nz0.3.A, 4nz0.5.A, 4nz0.6.A, 4o4r.1.A, 4oow.1.A, 4oow.2.A, 4qpx.1.A, 4r0e.1.A, 4ry4.1.A, 4ry4.2.A, 4ry5.1.A, 4ry5.2.A, 4ry6.1.A, 4ry7.1.A, 4ry7.2.A, 4tlr.1.A, 4tn2.1.A, 4txs.1.A, 4ty8.2.A, 4ty9.1.A, 4v0r.1.A, 4wfx.1.A, 4wfy.1.A, 4wt9.1.A, 4wtc.1.A, 4wtk.1.A, 4wyl.1.A, 4wyw.1.A, 4wzm.1.A, 4wzq.1.A, 4x2b.1.A, 4y2a.1.A, 4y2c.1.A, 4y34.1.A, 4y3c.1.A, 4y3c.2.A, 4y3c.3.A, 4y3c.5.A, 4y3c.6.A, 4zp6.1.A, 4zp7.1.A, 4zp8.1.A, 4zp9.1.A, 4zpa.1.A, 4zpb.1.A, 4zpc.1.A, 4zpd.1.A, 5ccv.1.A, 5ccv.2.A, 5ccv.3.A, 5ccv.5.A, 5ccv.8.A, 5czb.1.A, 5dto.1.A, 5f8g.1.A, 5i61.1.A, 5i61.2.A, 5i62.1.A, 5iq6.1.A, 5jjs.1.A, 5jxs.1.A, 5k5m.1.A, 5n8x.1.A, 5n95.1.A, 5pzo.1.A, 5pzo.2.A, 5pzp.2.A, 5qj0.1.A, 5qj1.1.A, 5tfr.1.A, 5tmh.1.A, 5twm.1.A, 5u0b.1.A, 5u0c.1.A, 5u0c.3.A, 5u0c.4.A, 5uj2.1.A, 5w2e.1.A, 5xe0.1.A, 5y6r.1.A, 5y6z.1.A, 5yf5.1.A, 5yf6.1.A, 5yf7.1.A, 5yf8.1.A, 5ziu.1.A, 5zqk.1.A, 6ae4.1.A, 6ae5.1.A, 6ae7.1.A, 6gp9.1.A, 6gvv.1.A, 6gvy.1.A, 6iii.1.A, 6izx.1.A, 6izy.1.A, 6izz.1.A, 6j00.1.A, 6kr2.1.A, 6kr3.1.A, 6kwq.1.A, 6ld1.1.A, 6ld2.1.A, 6lse.1.A, 6lsg.1.A, 6mvk.1.A, 6mvo.1.A, 6mvp.1.A, 6mvq.1.A, 6qwt.1.A, 6r1i.1.A, 6r1i.2.A, 6s2l.1.A, 6ux2.1.B, 6wcz.1.B, 6xez.1.A, 6xqb.1.A, 6yyt.1.A, 7b3b.1.A, 7b3c.1.A, 7b3d.1.A, 7btf.1.A, 7bv1.1.A, 7bw4.1.A, 7bzf.1.A, 7c2k.1.A, 7ctt.1.A, 7cxm.1.A, 7cxn.1.A, 7cyq.1.A, 7d4f.1.D, 7d6n.1.A, 7dfg.1.C, 7dfh.1.A, 7diy.1.B, 7doi.1.A, 7dok.1.C, 7dte.1.A, 7ed5.1.A, 7egq.1.A, 7egq.1.I, 7eiz.1.A, 7ekj.1.A, 7f0s.1.A, 7l1f.1.A, 7mc5.1.A, 7mc6.1.A, 7oyg.1.A, 7oyg.1.F, 7ozu.1.A, 7ozv.1.A, 7rdy.1.A, 7re0.1.A, 7re2.1.A, 7re3.1.A, 7thm.1.A, 7uo4.1.A, 7uo7.1.A, 7uo9.1.A, 7uob.1.A, 7uoe.1.A, 7xd8.1.A, 7ziu.1.A, 7ziu.2.A, 8c1n.1.A, 8c1n.1.B, 8c2p.1.A, 8fm9.1.M, 8g6r.1.A, 8gwb.1.A, 8gwe.1.A, 8gwf.1.A, 8gwg.1.A, 8gwi.1.A, 8gwn.1.A, 8gwo.1.A