SWISS-MODEL Homology Modelling Report

Model Building Report

This document lists the results for the homology modelling project submitted to SWISS-MODEL workspace on March 14, 2018, 8:50 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 2018-03-07, PDB release 2018-03-02) 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-3.48
-2.99
All Atom-1.49
Solvation0.25
Torsion-2.90

TemplateSeq IdentityOligo-stateFound byMethodResolutionSeq SimilarityRangeCoverageDescription
5j4z.74.A88.11monomerHHblitsELECTRON MICROSCOPY5.80Å0.571 - 2271.00Cytochrome c oxidase subunit 2

Target    MAYPLQLGLQDATSPIMEELTSFHDHTLMIVFLISSLVLYIISSMLTTKMTHTNTMDAQGVETIWTILPAAILVLIALPS
5j4z.74.A MAYPMQLGFQDATSPIMEELLHFHDHTLMIVFLISSLVLYIISLMLTTKLTHTSTMDAQEVETIWTILPAIILIMIALPS

Target LRILYMMDEINNPALTVKTMGHQWYWSYEYTDYEDLYFDSYMTPTSDLKPGELRLLEVDNRVVLPMELPIRMLISSEDVL
5j4z.74.A LRILYMMDEINNPSLTVKTMGHQWYWSYEYTDYEDLSFDSYMIPTSELKPGELRLLEVDNRVVLPMEMTVRMLISSEDVL

Target HSWAVPSLGLKTDAIPGRLNQATISSNRPGLFYGQCSEICGSNHSFMPIVLEMVPLKHFENWSASMI
5j4z.74.A PSWAVPSLGLKTDAIPGRLNQTTLMSTRPGLFYGQCSEICGSNHSFMPIVLELVPLKYFEKWSASML




Materials and Methods

Template Search

Template search with BLAST and HHBlits has been performed against the SWISS-MODEL template library (SMTL, last update: 2018-03-07, last included PDB release: 2018-03-02).

The target sequence was searched with BLAST against the primary amino acid sequence contained in the SMTL. A total of 20 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 327 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.

MAYPLQLGLQDATSPIMEELTSFHDHTLMIVFLISSLVLYIISSMLTTKMTHTNTMDAQGVETIWTILPAAILVLIALPSLRILYMMDEINNPALTVKTM
GHQWYWSYEYTDYEDLYFDSYMTPTSDLKPGELRLLEVDNRVVLPMELPIRMLISSEDVLHSWAVPSLGLKTDAIPGRLNQATISSNRPGLFYGQCSEIC
GSNHSFMPIVLEMVPLKHFENWSASMI

Table T2:

TemplateSeq IdentityOligo-stateFound byScoresMethodResolutionSeq SimilarityCoverageDescription
3abm.1.B88.55monomerHHblitsp_value=1.5e-83, score=528.1, e_value=1.8e-79, ss_score=29, prob=100X-ray1.95Å0.571.00Cytochrome c oxidase subunit 2
2occ.1.B88.55monomerHHblitsp_value=1.5e-83, score=528.1, e_value=1.8e-79, ss_score=29, prob=100X-ray2.30Å0.571.00CYTOCHROME C OXIDASE
5j4z.74.A88.11monomerHHblitsp_value=1.5e-84, score=534.2, e_value=1.7e-80, ss_score=29.2, prob=100EM5.80Å0.571.00Cytochrome c oxidase subunit 2
1qle.1.B33.78monomerHHblitsp_value=1.4e-76, score=491.2, e_value=1.6e-72, ss_score=25.7, prob=100X-ray3.00Å0.380.99CYTOCHROME C OXIDASE POLYPEPTIDE II
1m56.1.B34.67monomerHHblitsp_value=6.9e-78, score=502.9, e_value=8.1e-74, ss_score=26.8, prob=100X-ray2.30Å0.380.99CYTOCHROME C OXIDASE
3hb3.1.B33.93monomerHHblitsp_value=9.3e-80, score=522.6, e_value=1.1e-75, ss_score=26.8, prob=100X-ray2.25Å0.380.99Cytochrome c oxidase subunit 2
3om3.1.B34.82monomerHHblitsp_value=1.1e-79, score=511.8, e_value=1.3e-75, ss_score=26.5, prob=100X-ray2.60Å0.380.99Cytochrome c oxidase subunit 2
3fye.2.B34.82monomerHHblitsp_value=9.7e-77, score=495.1, e_value=1.1e-72, ss_score=27.1, prob=100X-ray2.15Å0.380.99Cytochrome C oxidase subunit 2
5weh.2.A34.82monomerHHblitsp_value=9.7e-77, score=495.1, e_value=1.1e-72, ss_score=27.1, prob=100X-ray3.45Å0.380.99Cytochrome c oxidase subunit 2
1m56.1.B43.20monomerBLASTe_value=6.86399e-31, bit_score=117.472, score=293X-ray2.30Å0.430.74CYTOCHROME C OXIDASE
3fye.2.B43.20monomerBLASTe_value=8.2959e-31, bit_score=117.087, score=292X-ray2.15Å0.430.74Cytochrome C oxidase subunit 2
5weh.2.A43.20monomerBLASTe_value=8.2959e-31, bit_score=117.087, score=292X-ray3.45Å0.430.74Cytochrome c oxidase subunit 2
3om3.1.B43.20monomerBLASTe_value=1.17855e-30, bit_score=116.701, score=291X-ray2.60Å0.430.74Cytochrome c oxidase subunit 2
1qle.1.B42.68monomerBLASTe_value=2.08549e-33, bit_score=123.635, score=309X-ray3.00Å0.430.72CYTOCHROME C OXIDASE POLYPEPTIDE II
3hb3.1.B42.68monomerBLASTe_value=2.60066e-33, bit_score=124.405, score=311X-ray2.25Å0.430.72Cytochrome c oxidase subunit 2
4txv.1.B43.07monomerHHblitsp_value=1.8e-60, score=365.3, e_value=2.2e-56, ss_score=15.8, prob=100X-ray2.00Å0.430.60Cytochrome c oxidase subunit 2
4txv.2.B43.07monomerHHblitsp_value=1.8e-60, score=365.3, e_value=2.2e-56, ss_score=15.8, prob=100X-ray2.00Å0.430.60Cytochrome c oxidase subunit 2
4w9z.1.A45.80monomerHHblitsp_value=1.6e-56, score=335, e_value=2e-52, ss_score=16.8, prob=100X-ray1.30Å0.440.58Cytochrome c oxidase subunit 2
4w9z.1.A50.41monomerBLASTe_value=4.70495e-41, bit_score=140.584, score=353X-ray1.30Å0.460.54Cytochrome c oxidase subunit 2
4txv.1.B49.59monomerBLASTe_value=1.50789e-39, bit_score=137.502, score=345X-ray2.00Å0.460.54Cytochrome c oxidase subunit 2
4txv.2.B49.59monomerBLASTe_value=1.50789e-39, bit_score=137.502, score=345X-ray2.00Å0.460.54Cytochrome c oxidase subunit 2
2lln.1.A21.65monomerHHblitsp_value=5.7e-28, score=165.3, e_value=6.7e-24, ss_score=12, prob=99.9NMRNA0.330.43Cytochrome c oxidase subunit 2
2cua.1.A21.65monomerHHblitsp_value=1.6e-27, score=164.7, e_value=1.8e-23, ss_score=12.2, prob=99.9X-ray1.60Å0.330.43PROTEIN (CUA)
2cua.2.A21.65monomerHHblitsp_value=1.6e-27, score=164.7, e_value=1.8e-23, ss_score=12.2, prob=99.9X-ray1.60Å0.330.43PROTEIN (CUA)
2fwl.1.B21.88monomerHHblitsp_value=1.6e-26, score=159, e_value=1.9e-22, ss_score=8.8, prob=99.9NMRNA0.330.42Cytochrome c oxidase subunit II
5u7n.2.A22.73monomerHHblitsp_value=4.7e-22, score=130.7, e_value=5.4e-18, ss_score=12.1, prob=99.7X-ray2.30Å0.330.39Cytochrome c oxidase subunit 2
5u7n.1.A22.73monomerHHblitsp_value=4.7e-22, score=130.7, e_value=5.4e-18, ss_score=12.1, prob=99.7X-ray2.30Å0.330.39Cytochrome c oxidase subunit 2
2ppa.1.A16.88monomerHHblitsp_value=0.001, score=30.2, e_value=11, ss_score=8.3, prob=62.6X-ray1.69Å0.300.34Copper-containing nitrite reductase
4ysc.1.A16.88monomerHHblitsp_value=0.0024, score=27.7, e_value=27, ss_score=7.3, prob=41.5X-ray2.03Å0.300.34Copper-containing nitrite reductase
2vn3.1.A19.23monomerHHblitsp_value=0.0026, score=27.3, e_value=29, ss_score=8.9, prob=50.3X-ray2.35Å0.290.34DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE
1l9p.1.A16.88monomerHHblitsp_value=0.0011, score=30, e_value=12, ss_score=8.4, prob=61.8X-ray1.75Å0.300.34COPPER-CONTAINING NITRITE REDUCTASE
1l9r.1.A16.88monomerHHblitsp_value=0.0012, score=29.7, e_value=14, ss_score=8.6, prob=61.1X-ray1.78Å0.300.34COPPER-CONTAINING NITRITE REDUCTASE
2e86.1.A16.88monomerHHblitsp_value=0.0013, score=29.4, e_value=15, ss_score=8.7, prob=60.4X-ray1.50Å0.300.34Copper-containing nitrite reductase
1l9o.1.A16.88monomerHHblitsp_value=0.0018, score=28.5, e_value=20, ss_score=8.5, prob=53.9X-ray1.70Å0.300.34COPPER-CONTAINING NITRITE REDUCTASE
1et8.1.A16.88monomerHHblitsp_value=0.0018, score=28.6, e_value=20, ss_score=7.2, prob=46.4X-ray1.80Å0.300.34NITRITE REDUCTASE
2xx1.1.A19.23monomerHHblitsp_value=0.00094, score=30.3, e_value=10, ss_score=7.4, prob=58.5X-ray3.00Å0.280.34DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE
3h4h.1.A16.88monomerHHblitsp_value=0.0023, score=27.7, e_value=26, ss_score=8.5, prob=49.9X-ray1.60Å0.290.34Copper-containing nitrite reductase
1gs7.1.A17.95monomerHHblitsp_value=0.00097, score=30.2, e_value=11, ss_score=8.6, prob=64.7X-ray1.85Å0.280.34DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE
5onx.1.A17.95monomerHHblitsp_value=0.0014, score=29.2, e_value=15, ss_score=8.4, prob=57.7X-ray1.60Å0.280.34Copper-containing nitrite reductase
2xwz.1.A19.48monomerHHblitsp_value=0.0024, score=27.6, e_value=27, ss_score=8.5, prob=49.1X-ray2.34Å0.290.34DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE
1ndt.1.A19.48monomerHHblitsp_value=0.0016, score=28.8, e_value=17, ss_score=7.6, prob=51.3X-ray2.10Å0.290.34PROTEIN (NITRITE REDUCTASE)
2vw4.1.A21.05monomerHHblitsp_value=0.0035, score=26.4, e_value=39, ss_score=7.4, prob=35.7X-ray1.90Å0.300.33DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE
1wa0.1.A21.33monomerHHblitsp_value=0.0014, score=29.1, e_value=16, ss_score=7.5, prob=52.6X-ray1.60Å0.300.33DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE
2fwl.1.B27.94monomerBLASTe_value=8.36676e-05, bit_score=41.9726, score=97NMRNA0.360.30Cytochrome c oxidase subunit II
2cua.1.A27.94monomerBLASTe_value=8.48477e-05, bit_score=41.9726, score=97X-ray1.60Å0.360.30PROTEIN (CUA)
1gs6.1.A7.59homo-trimerHHblitsp_value=0.00017, score=35.1, e_value=1.9, ss_score=7.1, prob=78.9X-ray2.20Å0.230.35DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE
2bp8.1.A6.41homo-trimerHHblitsp_value=0.00025, score=34.1, e_value=2.8, ss_score=7.2, prob=75.3X-ray1.90Å0.230.34DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE
1wa1.1.A7.79homo-trimerHHblitsp_value=0.00012, score=36, e_value=1.3, ss_score=7.3, prob=82X-ray1.65Å0.230.34DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE
2xwz.1.A7.79homo-trimerHHblitsp_value=4.9e-05, score=38.7, e_value=0.54, ss_score=7.8, prob=88.2X-ray2.34Å0.230.34DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE
2vw4.1.A7.79monomerHHblitsp_value=8.9e-05, score=36.9, e_value=0.99, ss_score=7.1, prob=83.7X-ray1.90Å0.230.34DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE