UV_opsin_invertebrate

SWISS-MODEL Homology Modelling Report

Model Building Report

This document lists the results for the homology modelling project "UV_opsin_invertebrate" submitted to SWISS-MODEL workspace on Nov. 25, 2019, 7:52 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, F.T., de Beer, T.A.P., Rempfer, C., Bordoli, L., Lepore, R., Schwede, T. SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res. 46(W1), W296-W303 (2018).
Guex, N., Peitsch, M.C., Schwede, T. Automated comparative protein structure modeling with SWISS-MODEL and Swiss-PdbViewer: A historical perspective. Electrophoresis 30, S162-S173 (2009).
Bienert, S., Waterhouse, A., de Beer, T.A.P., Tauriello, G., Studer, G., Bordoli, L., Schwede, T. The SWISS-MODEL Repository - new features and functionality. Nucleic Acids Res. 45, D313-D319 (2017).
Benkert, P., Biasini, M., Schwede, T. Toward the estimation of the absolute quality of individual protein structure models. Bioinformatics 27, 343-350 (2011).
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).

Results

The SWISS-MODEL template library (SMTL version 2019-11-21, PDB release 2019-11-01) was searched with BLAST (Camacho et al.) and HHBlits (Remmert et al.) for evolutionary related structures matching the target sequence in Table T1. For details on the template search, see Materials and Methods. Overall 414 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	QMEAN
	PDB	ProMod3 2.0.0	monomer	None	0.73	-3.27

Template	Seq Identity	Oligo-state	QSQE	Found by	Method	Resolution	Seq Similarity	Range	Coverage	Description
2z73.1.A	33.66	monomer	0.00	BLAST	X-ray	2.50Å	0.39	17 - 325	0.94	Rhodopsin

Excluded ligands

Ligand Name.Number	Reason for Exclusion	Description
BOG.1	Binding site not conserved.	B-OCTYLGLUCOSIDE
PLM.3	Binding site not conserved.	PALMITIC ACID
PLM.4	Binding site not conserved.	PALMITIC ACID
RET.2	Binding site not conserved.	RETINAL
TWT.5	Binding site not conserved.	DOCOSANE

Target    LLGAGLSGEELEMIPMHWRGQLAPPSVAHTGLALLYVWLTAAALIGNGLVLFIFTTSKSLHTASNLLVWNLALCDFI--M
2z73.1.A  ----------------HWREFDQVPDAVYYSLGIFIGICGIIGCGGNGIVIYLFTKTKSLQTPANMFIINLAFSDFTFSL

Target    MAKAPIFIYNSVLGGFASGTAGCKAFAFMGAYSGIVAGATNAAIAYDRHSTITRPL--DGRISRGKALLIVLMAWIYATP
2z73.1.A  VNGFPLMTISCFLKKWIFGFAACKVYGFIGGIFGFMSIMTMAMISIDRYNVIGRPMAASKKMSHRRAFIMIIFVWLWSVL

Target    WAVLPLLKVWGRFVPEGYLTSCSFDYLTRTFETQLFVACIFVCSYCLPLCFMMYFYSGIVKQVFAHEAALRAQAKKMNVE
2z73.1.A  WAIGPIFG-WGAYTLEGVLCNCSFDYISRDSTTRSNILCMFILGFFGPILIIFFCYFNIVMSVSNHEKEMAAMAKRLNAK

Target    SLRSNQNEAAESAEIRIAKAALTVCFLFLASWTPYGVMALIGAFGDQRMLTPGVTMIPAVACKLVACIDPWIYAISHPKY
2z73.1.A  ELRKAQ--AGANAEMRLAKISIVIVSQFLLSWSPYAVVALLAQFGPLEWVTPYAAQLPVMFAKASAIHNPMIYSVSHPKF

Target    RLELQKRMP
2z73.1.A  REAISQTFP

Materials and Methods

Template Search

Template search with BLAST and HHBlits has been performed against the SWISS-MODEL template library (SMTL, last update: 2019-11-21, last included PDB release: 2019-11-01).

The target sequence was searched with BLAST against the primary amino acid sequence contained in the SMTL. A total of 112 templates were found.

An initial HHblits profile has been built using the procedure outlined in (Remmert et al.), followed by 1 iteration of HHblits against NR20. The obtained profile has then be searched against all profiles of the SMTL. A total of 303 templates were found.

Model Building

Models are built based on the target-template alignment using ProMod3. 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. In case loop modelling with ProMod3 fails, an alternative model is built with PROMOD-II (Guex et al.).

Model Quality Estimation

The global and per-residue model quality has been assessed using the QMEAN scoring function (Benkert et al.) . For improved performance, weights of the individual QMEAN terms have been trained specifically for SWISS-MODEL.

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

BLAST
Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., Madden, T.L. BLAST+: architecture and applications. BMC Bioinformatics 10, 421-430 (2009).
HHblits
Remmert, M., Biegert, A., Hauser, A., Söding, J. HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nat Methods 9, 173-175 (2012).

Table T1:

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

LLGAGLSGEELEMIPMHWRGQLAPPSVAHTGLALLYVWLTAAALIGNGLVLFIFTTSKSLHTASNLLVWNLALCDFIMMAKAPIFIYNSVLGGFASGTAG
CKAFAFMGAYSGIVAGATNAAIAYDRHSTITRPLDGRISRGKALLIVLMAWIYATPWAVLPLLKVWGRFVPEGYLTSCSFDYLTRTFETQLFVACIFVCS
YCLPLCFMMYFYSGIVKQVFAHEAALRAQAKKMNVESLRSNQNEAAESAEIRIAKAALTVCFLFLASWTPYGVMALIGAFGDQRMLTPGVTMIPAVACKL
VACIDPWIYAISHPKYRLELQKRMP

Table T2:

Template	Seq Identity	Oligo-state	QSQE	Found by	Method	Resolution	Seq Similarity	Coverage	Description
2z73.1.A	33.66	monomer	-	BLAST	X-ray	2.50Å	0.39	0.94	Rhodopsin
2z73.1.A	33.01	monomer	-	HHblits	X-ray	2.50Å	0.38	0.94	Rhodopsin
6i9k.1.A	35.42	monomer	-	HHblits	X-ray	2.14Å	0.38	0.98	Kumopsin1
4ww3.1.A	33.66	monomer	-	BLAST	X-ray	2.80Å	0.39	0.94	Rhodopsin
6i9k.1.A	37.30	monomer	-	BLAST	X-ray	2.14Å	0.39	0.96	Kumopsin1
2ziy.1.A	33.66	monomer	-	BLAST	X-ray	3.70Å	0.39	0.94	Rhodopsin
4ww3.1.A	32.89	monomer	-	HHblits	X-ray	2.80Å	0.38	0.94	Rhodopsin
2ziy.1.A	33.11	monomer	-	HHblits	X-ray	3.70Å	0.38	0.94	Rhodopsin
6cmo.1.A	24.83	monomer	-	HHblits	EM	NA	0.33	0.89	chimera protein of Soluble cytochrome b562 and Rhodopsin
5w0p.1.A	24.83	monomer	-	HHblits	X-ray	3.01Å	0.33	0.89	Endolysin,Rhodopsin,S-arrestin
5dgy.2.A	24.74	monomer	-	HHblits	X-ray	7.70Å	0.33	0.90	Endolysin,Rhodopsin,S-arrestin
5iu7.1.A	20.88	monomer	-	HHblits	X-ray	1.90Å	0.31	0.91	Adenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a
6fk9.1.A	25.44	monomer	-	HHblits	X-ray	2.63Å	0.33	0.88	Rhodopsin
2j4y.1.A	25.44	homo-dimer	0.08	HHblits	X-ray	3.40Å	0.33	0.88	RHODOPSIN
6j21.1.A	19.06	monomer	-	HHblits	X-ray	3.20Å	0.30	0.92	Substance-P receptor,Endolysin
5dys.1.A	25.52	monomer	-	HHblits	X-ray	2.30Å	0.33	0.88	Rhodopsin
4u15.2.A	21.50	monomer	-	HHblits	X-ray	2.80Å	0.32	0.90	Muscarinic acetylcholine receptor M3,Lysozyme,Muscarinic acetylcholine receptor M3
5zhp.2.A	21.16	monomer	-	HHblits	X-ray	3.10Å	0.32	0.90	Muscarinic acetylcholine receptor M3,Endolysin,Endolysin,Muscarinic acetylcholine receptor M3
5zhp.1.A	21.16	monomer	-	HHblits	X-ray	3.10Å	0.32	0.90	Muscarinic acetylcholine receptor M3,Endolysin,Endolysin,Muscarinic acetylcholine receptor M3
5zbh.1.A	19.13	monomer	-	HHblits	X-ray	3.00Å	0.30	0.92	Neuropeptide Y receptor type 1,T4 Lysozyme,Neuropeptide Y receptor type 1
4u15.1.A	21.50	monomer	-	HHblits	X-ray	2.80Å	0.32	0.90	Muscarinic acetylcholine receptor M3,Lysozyme,Muscarinic acetylcholine receptor M3
6j20.1.A	18.73	monomer	-	HHblits	X-ray	2.70Å	0.30	0.92	Substance-P receptor,Endolysin
6e67.1.A	19.80	monomer	-	HHblits	X-ray	3.70Å	0.31	0.90	Beta-2 adrenergic receptor,Endolysin,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short,Beta-2 adrenergic receptor chimera
4u14.1.A	21.36	monomer	-	HHblits	X-ray	3.57Å	0.32	0.91	Muscarinic acetylcholine receptor M3,Endolysin,Muscarinic acetylcholine receptor M3
5cxv.1.A	19.87	monomer	-	HHblits	X-ray	2.70Å	0.31	0.91	Muscarinic acetylcholine receptor M1,Endolysin,Muscarinic acetylcholine receptor M1
4daj.2.A	21.09	monomer	-	HHblits	X-ray	3.40Å	0.32	0.90	Muscarinic acetylcholine receptor M3, Lysozyme
4dkl.1.A	17.51	homo-dimer	0.16	HHblits	X-ray	2.80Å	0.30	0.91	Mu-type opioid receptor, lysozyme chimera
4daj.1.A	21.09	monomer	-	HHblits	X-ray	3.40Å	0.32	0.90	Muscarinic acetylcholine receptor M3, Lysozyme
6me8.1.A	21.43	monomer	-	HHblits	X-ray	3.10Å	0.31	0.90	Soluble cytochrome b562,Melatonin receptor type 1B,Rubredoxin
6hlo.1.A	19.06	monomer	-	HHblits	X-ray	2.40Å	0.30	0.92	Substance-P receptor,GlgA glycogen synthase,Substance-P receptor
4djh.1.A	15.95	homo-dimer	0.11	HHblits	X-ray	2.90Å	0.30	0.93	Kappa-type opioid receptor, Lysozyme
4xnw.2.A	16.94	monomer	-	HHblits	X-ray	2.70Å	0.29	0.93	P2Y purinoceptor 1,Rubredoxin,P2Y purinoceptor 1
6hll.1.A	19.06	monomer	-	HHblits	X-ray	3.27Å	0.30	0.92	Substance-P receptor,GlgA glycogen synthase,Substance-P receptor
4djh.1.B	15.95	homo-dimer	0.11	HHblits	X-ray	2.90Å	0.30	0.93	Kappa-type opioid receptor, Lysozyme
4ej4.1.A	17.79	monomer	-	HHblits	X-ray	3.40Å	0.30	0.92	Delta-type opioid receptor, Lysozyme chimera
3sn6.1.D	19.87	monomer	-	HHblits	X-ray	3.20Å	0.31	0.91	Endolysin,Beta-2 adrenergic receptor
5zkp.1.A	18.06	monomer	-	HHblits	X-ray	2.81Å	0.30	0.92	Platelet-activating factor receptor,Flavodoxin,Platelet-activating factor receptor
6oij.1.B	20.61	monomer	-	HHblits	EM	NA	0.31	0.91	Muscarinic acetylcholine receptor M1
2x72.1.A	25.44	homo-dimer	0.05	HHblits	X-ray	3.00Å	0.33	0.88	RHODOPSIN
4xnw.1.A	16.94	monomer	-	HHblits	X-ray	2.70Å	0.29	0.93	P2Y purinoceptor 1,Rubredoxin,P2Y purinoceptor 1
4xnv.1.A	16.94	monomer	-	HHblits	X-ray	2.20Å	0.29	0.93	P2Y purinoceptor 1, Rubredoxin, P2Y purinoceptor 1
6me8.2.A	21.43	monomer	-	HHblits	X-ray	3.10Å	0.31	0.90	Soluble cytochrome b562,Melatonin receptor type 1B,Rubredoxin
4bez.1.A	25.44	homo-dimer	-	HHblits	X-ray	3.30Å	0.33	0.88	RHODOPSIN
3sn6.1.D	21.48	monomer	-	BLAST	X-ray	3.20Å	0.32	0.92	Endolysin,Beta-2 adrenergic receptor
3kj6.1.A	19.80	monomer	-	HHblits	X-ray	3.40Å	0.31	0.92	Beta-2 adrenergic receptor
2r4s.1.A	19.53	monomer	-	HHblits	X-ray	3.40Å	0.31	0.91	Beta-2 adrenergic receptor
2r4r.1.A	19.46	monomer	-	HHblits	X-ray	3.40Å	0.31	0.92	Beta-2 adrenergic receptor
3kj6.1.A	21.38	monomer	-	BLAST	X-ray	3.40Å	0.32	0.89	Beta-2 adrenergic receptor
2r4s.1.A	21.38	monomer	-	BLAST	X-ray	3.40Å	0.32	0.89	Beta-2 adrenergic receptor
2r4r.1.A	21.38	monomer	-	BLAST	X-ray	3.40Å	0.32	0.89	Beta-2 adrenergic receptor

The table above shows the top 50 filtered templates. A further 286 templates were found which were considered to be less suitable for modelling than the filtered list.
3oe9.1.A, 6gpx.1.A, 6jzh.1.A, 3oe9.1.B, 5n2s.1.A, 3zev.1.A, 6rz5.1.A, 2ycw.1.A, 2i35.1.A, 5tzy.1.A, 6meo.1.C, 4ej4.1.A, 5vew.1.A, 6g79.1.D, 5d5a.1.A, 6b73.1.A, 5zhp.1.A, 3pbl.1.A, 5wb1.1.A, 5uiw.1.A, 4iaq.1.A, 5uen.1.B, 2i37.1.A, 5wiu.1.A, 5uen.1.A, 3c9m.1.A, 1hof.1.A, 1jfp.1.A, 6me7.2.A, 6nbi.1.A, 6fuf.1.A, 4z35.1.A, 3oax.1.A, 6nbh.1.A, 5nx2.1.A, 4gpo.1.A, 4bwb.1.A, 3c9l.1.A, 6o3c.1.A, 6m9t.1.A, 6me2.1.A, 3oe6.1.A, 5dhg.1.A, 5te5.1.A, 4xnv.1.A, 5o9h.1.B, 5o9h.1.A, 5dgy.2.A, 5xez.1.A, 5l7d.1.A, 4ami.1.A, 5xjm.1.A, 2ycx.1.A, 4gbr.1.A, 3cap.1.A, 4zud.1.A, 6e67.1.A, 4buo.2.A, 6igk.1.A, 5nj6.1.A, 4bv0.1.A, 6me9.2.A, 5wf5.1.A, 5t1a.1.A, 6ibl.2.A, 3oe8.2.B, 6os9.1.A, 4k5y.1.A, 4o9r.1.A, 5zkq.1.A, 5zkq.1.B, 3vga.1.A, 5tgz.1.A, 6qzh.1.A, 1ho9.1.A, 5l7i.2.A, 6dry.1.A, 4buo.1.A, 5xr8.1.A, 5zk8.1.A, 1l9h.3.B, 6d26.1.A, 1ln6.1.A, 3pbl.2.A, 5ee7.1.A, 6fk9.1.A, 5wf6.1.A, 2lov.1.A, 4qim.1.A, 5glh.1.A, 5v57.1.A, 3p0g.1.A, 4grv.1.A, 3odu.1.B, 2ki9.1.A, 5v57.1.B, 6ibb.2.A, 6ak3.1.A, 6h7n.1.B, 6oya.1.E, 3qak.1.A, 4lde.1.A, 5uig.1.A, 1hll.1.A, 1hod.1.A, 4z9g.3.A, 6gdg.1.A, 6ibb.1.A, 4xt1.1.A, 4pxz.1.A, 6ofj.1.A, 3oe0.1.A, 2lnl.1.A, 6oy9.1.D, 6bqh.1.A, 1eds.1.A, 4u14.1.A, 5jtb.1.A, 2i36.1.A, 2ydo.1.A, 6igl.1.A, 4z34.1.A, 6e59.1.A, 5jqh.1.A, 2koe.1.A, 5unf.1.A, 5l7i.1.A, 5tud.1.A, 4n4w.1.A, 4bwb.2.A, 6ot0.1.A, 5f8u.1.A, 5zkb.1.A, 4bez.1.A, 4uhr.1.A, 4z36.1.A, 1edv.1.A, 5zty.1.A, 6oik.1.A, 3v2w.1.A, 6rnk.1.A, 6rz5.2.A, 4rwd.2.A, 6fkb.1.A, 5zhp.2.A, 5c1m.1.A, 6osa.1.A, 3rze.1.A, 1f88.1.A, 5dsg.2.A, 5kw2.1.A, 5unh.1.A, 4daj.1.A, 5unh.1.B, 6n4b.1.D, 3uzc.1.A, 6e3y.1.F, 5g53.1.A, 5dsg.1.A, 5dhh.2.A, 6me8.1.A, 3vg9.1.A, 3oe8.2.C, 3vw7.1.A, 5xra.1.A, 4rwa.1.A, 5lwe.1.A, 5gli.1.A, 3eml.1.A, 5vai.1.A, 4a4m.1.A, 4xes.1.A, 5dys.1.A, 4bv0.2.A, 4u15.2.A, 4djh.1.B, 1fdf.1.A, 4mbs.1.A, 6qno.1.F, 5lwe.2.A, 3ny8.1.A, 2x72.1.A, 4u15.1.A, 5xpr.1.A, 3pxo.1.A, 6aky.1.A, 2vt4.1.A, 5x33.1.A, 6a93.1.A, 6c1q.1.A, 6cm4.1.A, 2low.1.A, 4ea3.1.A, 6d35.1.A, 6d32.1.A, 4yay.1.A, 3pds.1.A, 4xnw.2.A, 2ycz.1.A, 5xez.2.A, 6do1.1.A, 6mxt.1.A, 5w0p.1.A, 5ndd.1.A, 4bvn.1.A, 6niy.1.C, 4k5y.2.A, 2lot.1.A, 2j4y.1.A, 6b3j.1.A, 4dkl.1.A, 4nc3.1.A, 6aqf.1.A, 4py0.1.A, 6dde.1.E, 5xsz.1.A, 6oij.1.B, 4iar.1.A, 6rz4.1.A, 5a8e.1.A, 6nbf.1.A, 4xee.1.A, 6mh8.1.A, 4jkv.1.A, 6a93.2.A, 6iiu.1.A, 4ib4.1.A, 5wqc.1.A, 4jkv.1.B, 6drz.1.A, 4ntj.1.A, 6me6.1.B, 6me6.1.A, 5t04.1.A, 5v54.1.B, 4xnw.1.A, 4z9g.1.A, 4z9g.2.A, 4qkx.1.A, 6akx.1.A, 5ung.1.A, 5x7d.1.A, 4qin.1.A, 5yqz.1.A, 6drx.1.A, 4ug2.1.A, 6d9h.1.D, 5vbl.1.B, 6gps.1.A, 6cmo.1.A, 4rws.1.A, 5ywy.1.A, 4k5y.3.A, 4n6h.1.A, 4djh.1.A, 3oe8.3.A, 2ks9.1.A, 5cxv.1.A, 3odu.1.A, 5l7d.2.A, 6bqg.1.A, 6me8.2.A, 5zbq.1.A, 6k1q.1.A, 1f88.1.B, 5u09.1.A, 6ibl.1.A, 5mzj.1.A, 6me7.1.A, 4zj8.1.A, 6e67.2.A, 5yc8.1.A, 6bd4.1.A, 5tvn.1.A, 4s0v.1.A, 6fk6.1.A, 5wb2.1.A, 4mqs.1.A, 5v54.1.A, 5uz7.1.E, 5tzr.1.A, 4xt3.1.A, 4l6r.1.A, 2lou.1.A, 3uon.1.A, 4daj.2.A