SWISS-MODEL Homology Modelling Report

Model Building Report

This document lists the results for the homology modelling project submitted to SWISS-MODEL workspace on Dec. 23, 2018, 11:52 a.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 2018-12-17, PDB release 2018-11-30) 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 50 templates were found (Table T2).

Models

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

FileBuilt withOligo-StateLigandsQMEAN
PDBProMod3Monomer
QMEAN-4.92
-3.49
All Atom-2.00
Solvation-0.60
Torsion-4.12

TemplateSeq IdentityOligo-stateFound byMethodResolutionSeq SimilarityRangeCoverageDescription
1wp9.1.A21.06monomerHHblitsX-RAY DIFFRACTION2.90Å0.3020 - 4920.31ATP-dependent RNA helicase, putative

Target    RIGVVDKGIHQYTDLSFVLQFLHYYTCSFSKFRNFSVTFSIISAFFLVCFTQQAEALKMHTDL---KVGMYWGDMGVDFW
1wp9.1.A CLIVLPTGLGK--TLIAMMIAEYRLT--------KYGGKVLMLAPTKPLVLQHAESFRRLFNLPPEKIVALTGEKSPE--

Target DSSTWKQEVDKYEVLVMTPAILLDALRHSFLSLSMIKVLIVDECHHAGGKHPYACIMREFYHKELNSGTSNVPRIFGMTA
1wp9.1.A ---ERSKAWARAKVIVATPQTIENDLLAGRISLEDVSLIVFDEAHRAVGNYAYVFIAREYK-R-----QAKNPLVIGLTA

Target SLVKTKGENLDSYWKKIHELETLMNS-KVYTCE-NESVLAGFVPFSTPSFKYYQHIKIPSPKRASLVEKLERLTIKHRLS
1wp9.1.A SPGSTP--------EKIMEVINNLGIEHIEYRSENSPDVRPYVKGIRFEWVRVD---LPEIY-KEVRKLLREMLRDALKP

Target LGTLDLNS-STVDSVEKRLLRISSTLTYCL--DDLGILLAQKAAQSLSASQNDSFLWGELNMFSVALVKKFCSDASQEFL
1wp9.1.A LAETGLLESSSPDIPKKEVLRAGQIINEEMAKGNHDLRGLLLYHAMALKLHHAIE---LLETQGLSALRAYIKKLYEEAK

Target AEI-PQGLNWSVA----NIN---G-NAEAGLLTLKTVCLIETLLGYS-SLENIRCIIFVDRVITAIVLESLLAEILPNCN
1wp9.1.A AGSTKASKEIFSDKRMKKAISLLVQAKEIGLDHPKMDKLKEIIREQLQRKQNSKIIVFTNYRETAKKIVNELVKD-----

Target NWKTKYVAGNNSG--LQNQTRKKQNEIVEDFRRGLVNIIVATSILEEGLDVQSCNLVIRFDPASNICSFIQSRGRARMQN
1wp9.1.A GIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNVLVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGRHM

Target SD-YLMMVESGDLL
1wp9.1.A PGRVIILMAKGTRD




Materials and Methods

Template Search

Template search with BLAST and HHBlits has been performed against the SWISS-MODEL template library (SMTL, last update: 2018-12-17, last included PDB release: 2018-11-30).

The target sequence was searched with BLAST against the primary amino acid sequence contained in the SMTL. A total of 97 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 1096 templates were found.

Template Selection

For each identified template, the template's quality has been predicted from features of the target-template alignment. The templates with the highest quality have then been selected for model building.

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

Table T1:

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

MLLCLLGSSSGSCHSGIGVRIGVVDKGIHQYTDLSFVLQFLHYYTCSFSKFRNFSVTFSIISAFFLVCFTQQAEALKMHTDLKVGMYWGDMGVDFWDSST
WKQEVDKYEVLVMTPAILLDALRHSFLSLSMIKVLIVDECHHAGGKHPYACIMREFYHKELNSGTSNVPRIFGMTASLVKTKGENLDSYWKKIHELETLM
NSKVYTCENESVLAGFVPFSTPSFKYYQHIKIPSPKRASLVEKLERLTIKHRLSLGTLDLNSSTVDSVEKRLLRISSTLTYCLDDLGILLAQKAAQSLSA
SQNDSFLWGELNMFSVALVKKFCSDASQEFLAEIPQGLNWSVANINGNAEAGLLTLKTVCLIETLLGYSSLENIRCIIFVDRVITAIVLESLLAEILPNC
NNWKTKYVAGNNSGLQNQTRKKQNEIVEDFRRGLVNIIVATSILEEGLDVQSCNLVIRFDPASNICSFIQSRGRARMQNSDYLMMVESGDLLTQSRLMKY
LSGGKRMREESLDHSLVPCPPLPDDSDEPLFRVESTGATVTLSSSVSLIYHYCSRLPSDEYFKPAPRFDVNKDQGSCTLYLPKSCPVKEVKAEANNKVLK
QAVCLKACIQLHKVGALSDHLVPDMVVAETVSQKLEKIQYNTEQPCYFPPELVSQFSAQPETTYHFYLIRMKPNSPRNFHLNDVLLGTRVVLEDDIGNTS
FRLEDHRGTIAVTLSYVGAFHLTQEEVLFCRRFQITLFRVLLDHSVENLMEALNGLHLRDGVALDYLLVPSTHSHETSLIDWEVIRSVNLTSHEVLEKHE
NCSTNGASRILHTKDGLFCTCVVQNALVYTPHNGYVYCTKGVLNNLNGNSLLTKRNSGDQTYIEYYEERHGIQLNFVDEPLLNGRHIFTLHSYLHMAKKK
KEKEHDREFVELPPELCHVILSPISVDMIYSYTFIPSVMQRIESLLIAYNLKKSIPKVNIPTIKVLEAITTKKCEDQFHLESLETLGDSFLKYAVCQQLF
QHCHTHHEGLLSTKKDGMISNVMLCQFGCQQKLQGFIRDECFEPKGWMVPGQSSAAYSLVNDTLPESRNIYVASRRNLKRKSVADVVESLIGAYLSEGGE
LAALMFMNWVGIKVDFTTTKIQRDSPIQAEKLVNVGYMESLLNYSFEDKSLLVEALTHGSYMMPEIPRCYQRLEFLGDSVLDYLITKHLYDKYPCLSPGL
LTDMRSASVNNECYALVAVKANLHKHILYASHHLHKHISRTVSEFEQSSLQSTFGWESDISFPKVLGDVIESLAGAIFVDSGYNKEVVFASIKPLLGCMI
TPETVKLHPVRELTELCQKWQFELSKAKDFDSFTVEVKAKEMSFAHTAKASDKKMAKKLAYKEVLNLLKNSLDY

Table T2:

TemplateSeq IdentityOligo-stateFound byScoresMethodResolutionSeq SimilarityCoverageDescription
5zal.1.A27.76monomerHHblitsp_value=3e-184, score=1851.3, e_value=4e-180, ss_score=55.2, prob=100EMNA0.330.94Endoribonuclease Dicer
5zam.1.A27.76monomerHHblitsp_value=3e-184, score=1851.3, e_value=4e-180, ss_score=55.2, prob=100EMNA0.330.94Endoribonuclease Dicer
5zak.1.A27.76monomerHHblitsp_value=3e-184, score=1851.3, e_value=4e-180, ss_score=55.2, prob=100EMNA0.330.94Endoribonuclease Dicer
6bua.1.A23.66monomerHHblitsp_value=3e-189, score=1893, e_value=4e-185, ss_score=55.5, prob=100EMNA0.310.95Dicer-2, isoform A
2ffl.1.A20.17monomerHHblitsp_value=5.6e-93, score=864.2, e_value=7.1e-89, ss_score=9.6, prob=100X-ray3.33Å0.290.42Dicer
2ffl.5.B20.17homo-dimerHHblitsp_value=5.6e-93, score=864.2, e_value=7.1e-89, ss_score=9.6, prob=100X-ray3.33Å0.290.42Dicer
6bua.1.A27.78monomerBLASTe_value=4.79447e-42, bit_score=170.244, score=430EMNA0.350.39Dicer-2, isoform A
6gjz.1.A20.73monomerHHblitsp_value=3.1e-48, score=470, e_value=3.8e-44, ss_score=25.1, prob=100EMNA0.310.32Interferon-induced helicase C domain-containing protein 1
6gkh.1.A20.73monomerHHblitsp_value=3.1e-48, score=470, e_value=3.8e-44, ss_score=25.1, prob=100EMNA0.310.32Interferon-induced helicase C domain-containing protein 1
5e3h.1.A21.64monomerHHblitsp_value=6.3e-49, score=463.7, e_value=7.4e-45, ss_score=25.6, prob=100X-ray2.70Å0.300.32Probable ATP-dependent RNA helicase DDX58
5jb2.1.A20.14monomerHHblitsp_value=2.9e-48, score=456.6, e_value=3.4e-44, ss_score=26.4, prob=100X-ray2.20Å0.300.31LGP2
5f9f.1.E21.64homo-hexamerHHblitsp_value=6.3e-49, score=463.7, e_value=7.4e-45, ss_score=25.6, prob=100X-ray2.60Å0.300.32Probable ATP-dependent RNA helicase DDX58
6gpg.1.C21.69monomerHHblitsp_value=7e-48, score=455.2, e_value=8.3e-44, ss_score=25.6, prob=100X-ray2.89Å0.300.32Probable ATP-dependent RNA helicase DDX58
6h66.1.A20.73monomerHHblitsp_value=3.1e-48, score=470, e_value=3.8e-44, ss_score=25.1, prob=100EMNA0.310.32Interferon-induced helicase C domain-containing protein 1
6g1s.1.A20.68monomerHHblitsp_value=8.4e-48, score=452.9, e_value=1e-43, ss_score=26.4, prob=100EM3.93Å0.300.32Interferon-induced helicase C domain-containing protein 1
6h61.1.A20.73monomerHHblitsp_value=3.1e-48, score=470, e_value=3.8e-44, ss_score=25.1, prob=100EMNA0.310.32Interferon-induced helicase C domain-containing protein 1
5jaj.1.A20.19monomerHHblitsp_value=9.5e-49, score=461.2, e_value=1.1e-44, ss_score=26.2, prob=100X-ray1.50Å0.300.31LGP2
5jc7.1.A19.13homo-dimerHHblitsp_value=3.8e-49, score=465.9, e_value=4.5e-45, ss_score=24.6, prob=100X-ray2.75Å0.300.32Melanoma differentiation associated protein-5
5jc3.1.A19.13monomerHHblitsp_value=3.8e-49, score=465.9, e_value=4.5e-45, ss_score=24.6, prob=100X-ray2.60Å0.300.32Melanoma differentiation associated protein-5
6g19.1.A20.68monomerHHblitsp_value=5.1e-47, score=445.9, e_value=6e-43, ss_score=25.9, prob=100EM3.68Å0.310.32Interferon-induced helicase C domain-containing protein 1
5f9f.1.E26.92homo-hexamerBLASTe_value=1.44439e-18, bit_score=92.4337, score=228X-ray2.60Å0.340.28Probable ATP-dependent RNA helicase DDX58
5f98.1.C21.64homo-hexamerHHblitsp_value=6.3e-49, score=463.7, e_value=7.4e-45, ss_score=25.6, prob=100X-ray3.28Å0.300.32Probable ATP-dependent RNA helicase DDX58
3tbk.1.A20.05monomerHHblitsp_value=1.1e-38, score=358.3, e_value=1.2e-34, ss_score=23.4, prob=100X-ray2.14Å0.300.32RIG-I Helicase Domain
5jbj.1.A20.14monomerHHblitsp_value=2.9e-48, score=456.6, e_value=3.4e-44, ss_score=26.4, prob=100X-ray3.58Å0.300.31LGP2
5f98.1.E21.64homo-hexamerHHblitsp_value=6.3e-49, score=463.7, e_value=7.4e-45, ss_score=25.6, prob=100X-ray3.28Å0.300.32Probable ATP-dependent RNA helicase DDX58
4gl2.2.A20.63monomerHHblitsp_value=4.4e-49, score=465.1, e_value=5.2e-45, ss_score=25.5, prob=100X-ray3.56Å0.300.32Interferon-induced helicase C domain-containing protein 1
4gl2.1.A20.63monomerHHblitsp_value=4.4e-49, score=465.1, e_value=5.2e-45, ss_score=25.5, prob=100X-ray3.56Å0.300.32Interferon-induced helicase C domain-containing protein 1
1wp9.1.A21.06monomerHHblitsp_value=2.2e-34, score=314.7, e_value=2.4e-30, ss_score=20.4, prob=100X-ray2.90Å0.300.31ATP-dependent RNA helicase, putative
4a36.2.A20.83monomerHHblitsp_value=2.5e-40, score=373.6, e_value=2.8e-36, ss_score=26.1, prob=100X-ray3.70Å0.310.31RETINOIC ACID INDUCIBLE PROTEIN I
5e3h.1.A26.92monomerBLASTe_value=1.44439e-18, bit_score=92.4337, score=228X-ray2.70Å0.340.28Probable ATP-dependent RNA helicase DDX58
1wp9.2.A21.06monomerHHblitsp_value=2.2e-34, score=314.7, e_value=2.4e-30, ss_score=20.4, prob=100X-ray2.90Å0.300.31ATP-dependent RNA helicase, putative
6g1x.1.A20.68monomerHHblitsp_value=5.1e-47, score=445.9, e_value=6e-43, ss_score=25.9, prob=100EM3.93Å0.310.32Interferon-induced helicase C domain-containing protein 1
4on9.1.A20.68monomerHHblitsp_value=5.9e-39, score=363.5, e_value=6.7e-35, ss_score=23.3, prob=100X-ray2.71Å0.300.32Probable ATP-dependent RNA helicase DDX58
4a2w.1.A22.30monomerHHblitsp_value=2.8e-46, score=450.9, e_value=3.3e-42, ss_score=26.4, prob=100X-ray3.70Å0.310.32RETINOIC ACID INDUCIBLE PROTEIN I
3zd6.1.A20.97monomerHHblitsp_value=1e-48, score=461.9, e_value=1.2e-44, ss_score=25, prob=100X-ray2.80Å0.300.32PROBABLE ATP-DEPENDENT RNA HELICASE DDX58
2ykg.1.A21.14monomerHHblitsp_value=6.9e-49, score=463.4, e_value=8.1e-45, ss_score=25.6, prob=100X-ray2.50Å0.300.32PROBABLE ATP-DEPENDENT RNA HELICASE DDX58
4bpb.1.A20.73monomerHHblitsp_value=1.7e-48, score=460, e_value=2e-44, ss_score=25.8, prob=100X-ray2.58Å0.300.32PROBABLE ATP-DEPENDENT RNA HELICASE DDX58
4ay2.1.A21.41monomerHHblitsp_value=1.4e-48, score=459.9, e_value=1.7e-44, ss_score=25.5, prob=100X-ray2.80Å0.300.32PROBABLE ATP-DEPENDENT RNA HELICASE DDX58
4a2w.2.A22.30monomerHHblitsp_value=2.8e-46, score=450.9, e_value=3.3e-42, ss_score=26.4, prob=100X-ray3.70Å0.310.32RETINOIC ACID INDUCIBLE PROTEIN I
4a2q.1.A21.06monomerHHblitsp_value=1.2e-43, score=420.2, e_value=1.5e-39, ss_score=25.8, prob=100X-ray3.40Å0.310.31RETINOIC ACID INDUCIBLE PROTEIN I
6gpg.1.C26.92monomerBLASTe_value=1.33714e-18, bit_score=92.8189, score=229X-ray2.89Å0.340.28Probable ATP-dependent RNA helicase DDX58
5f98.1.C26.92homo-hexamerBLASTe_value=1.44439e-18, bit_score=92.4337, score=228X-ray3.28Å0.340.28Probable ATP-dependent RNA helicase DDX58
4a2q.3.A21.06monomerHHblitsp_value=1.2e-43, score=420.2, e_value=1.5e-39, ss_score=25.8, prob=100X-ray3.40Å0.310.31RETINOIC ACID INDUCIBLE PROTEIN I
6bu9.1.A23.66monomerHHblitsp_value=3e-189, score=1893, e_value=4e-185, ss_score=55.5, prob=100EMNA0.310.95Dicer-2, isoform A
5f98.1.E26.92homo-hexamerBLASTe_value=1.44439e-18, bit_score=92.4337, score=228X-ray3.28Å0.340.28Probable ATP-dependent RNA helicase DDX58
4on9.1.A26.92monomerBLASTe_value=2.62697e-18, bit_score=91.2781, score=225X-ray2.71Å0.340.28Probable ATP-dependent RNA helicase DDX58
4on9.2.A20.68monomerHHblitsp_value=5.9e-39, score=363.5, e_value=6.7e-35, ss_score=23.3, prob=100X-ray2.71Å0.300.32Probable ATP-dependent RNA helicase DDX58
6bu9.1.A27.78monomerBLASTe_value=4.79447e-42, bit_score=170.244, score=430EMNA0.350.39Dicer-2, isoform A
4a2p.1.A20.83monomerHHblitsp_value=2.5e-40, score=373.6, e_value=2.8e-36, ss_score=26.1, prob=100X-ray3.00Å0.310.31RETINOIC ACID INDUCIBLE PROTEIN I
4ay2.1.A26.92monomerBLASTe_value=1.32783e-18, bit_score=92.8189, score=229X-ray2.80Å0.340.28PROBABLE ATP-DEPENDENT RNA HELICASE DDX58