D-I-TASSER Q8WXH2

D-I-TASSER results for Q8WXH2

[Click result.zip to download all results on this page]

Summary of the Protein

Uniprot ID: Q8WXH2
Protein Name: Junctophilin-3
Gene Name: JPH3

Input Sequence in FASTA format

>Q8WXH2 (748 residues)
MSSGGRFNFDDGGSYCGGWEDGKAHGHGVCTGPKGQGEYTGSWSHGFEVLGVYTWPSGNT
YQGTWAQGKRHGIGLESKGKWVYKGEWTHGFKGRYGVRECAGNGAKYEGTWSNGLQDGYG
TETYSDGGTYQGQWVGGMRQGYGVRQSVPYGMAAVIRSPLRTSINSLRSEHTNGTALHPD
ASPAVAGSPAVSRGGFVLVAHSDSEILKSKKKGLFRRSLLSGLKLRKSESKSSLASQRSK
QSSFRSEAGMSTVSSTASDIHSTISLGEAEAELAVIEDDIDATTTETYVGEWKNDKRSGF
GVSQRSDGLKYEGEWASNRRHGYGCMTFPDGTKEEGKYKQNILVGGKRKNLIPLRASKIR
EKVDRAVEAAERAATIAKQKAEIAASRTSHSRAKAEAALTAAQKAQEEARIARITAKEFS
PSFQHRENGLEYQRPKRQTSCDDIEVLSTGTPLQQESPELYRKGTTPSDLTPDDSPLQSF
PTSPAATPPPAPAARNKVAHFSRQVSVDEERGGDIQMLLEGRAGDCARSSWGEEQAGGSR
GVRSGALRGGLLVDDFRTRGSGRKQPGNPKPRERRTESPPVFTWTSHHRASNHSPGGSRL
LELQEEKLSNYRMEMKPLLRMETHPQKRRYSKGGACRGLGDDHRPEDRGFGVQRLRSKAQ
NKENFRPASSAEPAVQKLASLRLGGAEPRLLRWDLTFSPPQKSLPVALESDEENGDELKS
STGSAPILVVMVILLNIGVAILFINFFI

Predicted Contact and Distance Map Used in D-I-TASSER simulation

Contact Map

Distance Map

D-I-TASSER simulation is guided by the consensus contact map (left figure) and distance map (right figure) derived based on confidence scores of DeepPotential. In the contact, distance map and hydrogen bond networks, the axes mark the residue index along the sequence. For the contact map, each dot represents a residue pair with predicted contact, while for the distance map and hydrogen bond network, a color scale represents a distance of 1-20+ angstroms or a angle of 0-180 degree.

Information of Domain

No. of Domain	Domain	Domain Boundary	Length of Domain	Models of Domain	Sequence
1	Q8WXH2-D1	1-155	155		MSSGGRFNFDDGGSYCGGWEDGKAHGHGVCTGPKGQGEYTGSWSHGFEVLGVYTWPSGNTYQGTWAQGKRHGIGLESKGKWVYKGEWTHGFKGRYGVRECAGNGAKYEGTWSNGLQDGYGTETYSDGGTYQGQWVGGMRQGYGVRQSVPYGMAAV
2	Q8WXH2-D2	156-276	121		IRSPLRTSINSLRSEHTNGTALHPDASPAVAGSPAVSRGGFVLVAHSDSEILKSKKKGLFRRSLLSGLKLRKSESKSSLASQRSKQSSFRSEAGMSTVSSTASDIHSTISLGEAEAELAVI
3	Q8WXH2-D3	277-352	76		EDDIDATTTETYVGEWKNDKRSGFGVSQRSDGLKYEGEWASNRRHGYGCMTFPDGTKEEGKYKQNILVGGKRKNLI
4	Q8WXH2-D4	353-748	396		PLRASKIREKVDRAVEAAERAATIAKQKAEIAASRTSHSRAKAEAALTAAQKAQEEARIARITAKEFSPSFQHRENGLEYQRPKRQTSCDDIEVLSTGTPLQQESPELYRKGTTPSDLTPDDSPLQSFPTSPAATPPPAPAARNKVAHFSRQVSVDEERGGDIQMLLEGRAGDCARSSWGEEQAGGSRGVRSGALRGGLLVDDFRTRGSGRKQPGNPKPRERRTESPPVFTWTSHHRASNHSPGGSRLLELQEEKLSNYRMEMKPLLRMETHPQKRRYSKGGACRGLGDDHRPEDRGFGVQRLRSKAQNKENFRPASSAEPAVQKLASLRLGGAEPRLLRWDLTFSPPQKSLPVALESDEENGDELKSSTGSAPILVVMVILLNIGVAILFINFFI

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.596

(a)

D-I-TASSER simulations generate a large ensemble of structural conformations, i.e. decoys. These decoys are clustered by SPICKER based on pairwise structure similarity to report up to five final models from the five largest clusters. Models are ranked in descending order of cluster size. If the simulations converge well, it is possible to have less than 5 models generated, which is usually an indication of good model quality.

(b)

The model confidence is quantitatified by estimated TM-score (eTM-score), calculated based on significance of threading template alignments, contact map satisfaction rate, mean absolute error between distance of model and distance of DeepPotential, and convergence of D-I-TASSER simulations. eTM-score is typically in the range of [0, 1], with higher eTM-score signifies higher model confidence.

Proteins with similar structure

Top 10 structural analogs in PDB (as identified by TM-align)

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	7rw4A	0.42	1.83	0.726	0.429	model1_7rw4A.pdb.gz
2	7oriA	0.31	8.42	0.035	0.503	model1_7oriA.pdb.gz
3	6uebA	0.28	8.58	0.024	0.459	model1_6uebA.pdb.gz
4	7pw4A	0.28	8.06	0.041	0.439	model1_7pw4A.pdb.gz
5	5a22A	0.28	8.60	0.034	0.453	model1_5a22A.pdb.gz
6	1vw1A	0.28	8.32	0.031	0.437	model1_1vw1A.pdb.gz
7	6l42A1	0.28	7.96	0.035	0.425	model1_6l42A1.pdb.gz
8	6pzkA	0.28	8.46	0.034	0.444	model1_6pzkA.pdb.gz
9	5h64A	0.27	8.17	0.027	0.432	model1_5h64A.pdb.gz
10	7yerA	0.27	8.58	0.032	0.443	model1_7yerA.pdb.gz

(a)	Query structure is shown in cartoon, while the structural analog is displayed using backbone trace.
(b)	Ranking of proteins is based on TM-score of the structural alignment between the query structure and known structures in the PDB library.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov. represents the coverage of the alignment by TM-align and is equal to the number of structurally aligned residues divided by length of the query protein.

Predicted Gene Ontology (GO) Terms

Molecular Function (MF)

GO term	Cscore^GO	Name
GO:0004871	0.40	signal transducer activity
GO:0043167	0.39	ion binding
GO:0005215	0.38	transporter activity
GO:0004872	0.38	receptor activity
GO:0099600	0.37	transmembrane receptor activity
GO:0038023	0.37	signaling receptor activity
GO:0046873	0.36	metal ion transmembrane transporter activity
GO:0022836	0.36	gated channel activity
GO:0005216	0.36	ion channel activity
GO:0004888	0.36	transmembrane signaling receptor activity
GO:0015276	0.35	ligand-gated ion channel activity
GO:0005262	0.35	calcium channel activity
GO:0015278	0.34	calcium-release channel activity
GO:0008289	0.34	lipid binding
GO:0035091	0.33	phosphatidylinositol binding
GO:0080025	0.32	phosphatidylinositol-3,5-bisphosphate binding
GO:0070300	0.32	phosphatidic acid binding
GO:0070273	0.32	phosphatidylinositol-4-phosphate binding
GO:0032266	0.32	phosphatidylinositol-3-phosphate binding
GO:0010314	0.32	phosphatidylinositol-5-phosphate binding
GO:0005547	0.32	phosphatidylinositol-3,4,5-trisphosphate binding
GO:0005546	0.32	phosphatidylinositol-4,5-bisphosphate binding
GO:0001786	0.32	phosphatidylserine binding
GO:0097159	0.30	organic cyclic compound binding

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Molecular Function. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Biological Process (BP)

GO term	Cscore^GO	Name
GO:0044699	0.93	single-organism process
GO:0065007	0.85	biological regulation
GO:0050789	0.84	regulation of biological process
GO:0050794	0.83	regulation of cellular process
GO:0009987	0.77	cellular process
GO:0065008	0.71	regulation of biological quality
GO:0044763	0.69	single-organism cellular process
GO:0023051	0.69	regulation of signaling
GO:0010646	0.69	regulation of cell communication
GO:0051049	0.67	regulation of transport
GO:0065009	0.66	regulation of molecular function
GO:0009966	0.63	regulation of signal transduction
GO:1902531	0.62	regulation of intracellular signal transduction
GO:0060341	0.61	regulation of cellular localization
GO:0060314	0.60	regulation of ryanodine-sensitive calcium-release channel activity

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Biological Process. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Cellular Component (CC)

GO term	Cscore^GO	Name
GO:0044464	1.00	cell part
GO:0044424	0.96	intracellular part
GO:0044444	0.88	cytoplasmic part
GO:0016020	0.76	membrane
GO:0044422	0.71	organelle part
GO:0044446	0.65	intracellular organelle part
GO:0044425	0.59	membrane part
GO:0043226	0.58	organelle
GO:0043229	0.56	intracellular organelle
GO:0043227	0.56	membrane-bounded organelle
GO:0043231	0.54	intracellular membrane-bounded organelle
GO:0032991	0.53	macromolecular complex
GO:0043234	0.52	protein complex
GO:0005789	0.51	endoplasmic reticulum membrane

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Cellular Component. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Predicted Enzyme Commission (EC) Numbers

Top 5 enzyme homologs in PDB

Rank	Cscore^EC	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	EC Number	Predicted Active Site Residues
1	0.060	2c4mC	0.239	8.80	0.054	0.401	2.4.1.1	NA
2	0.060	3b9jC	0.194	8.27	0.035	0.307	1.17.3.2 1.17.1.4	NA
3	0.060	2vz8A	0.248	8.50	0.051	0.404	2.3.1.85	NA
4	0.060	1fo4A	0.237	8.25	0.028	0.370	1.17.1.4	NA
5	0.060	3btaA	0.229	7.94	0.025	0.353	3.4.24.69	NA

	Click on the radio buttons to visualize predicted active site residues.
(a)	Cscore^EC is the confidence score for the Enzyme Commission (EC) number prediction. Cscore^EC values range in between [0-1]; where a higher score indicates a more reliable EC number prediction.
(b)	TM-score is a measure of global structural similarity between query and template protein.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov. represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

Predicted Ligand Binding Sites

Template proteins with similar binding site:

Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
1	0.01	2vdoA	0.178	6.98	0.024	0.257	0.49	III	complex1.pdb.gz	14,29,30,40
2	0.01	3ijeA	0.249	7.69	0.040	0.376	0.53	UUU	complex2.pdb.gz	41,50,52,62
3	0.01	1n38A	0.262	8.59	0.032	0.428	0.68	CH1	complex3.pdb.gz	23,26,27,28,29
4	0.01	2vdqA	0.177	7.08	0.024	0.254	0.48	III	complex4.pdb.gz	47,65,71,89
5	0.01	3ijeA	0.249	7.69	0.040	0.376	0.40	UUU	complex5.pdb.gz	40,46,47,49
6	0.01	1llwA	0.242	8.95	0.025	0.408	0.49	F3S	complex6.pdb.gz	50,51,52,53,74
7	0.01	1llzA	0.229	8.64	0.017	0.380	0.46	F3S	complex7.pdb.gz	50,51,52,53,63
8	0.01	1lm1A	0.233	8.29	0.028	0.369	0.71	F3S	complex8.pdb.gz	27,28,29,30,41,411
9	0.01	1tyeA	0.174	6.88	0.028	0.246	0.65	UUU	complex9.pdb.gz	19,41,45

	Click on the radio buttons to visualize predicted binding site and residues.
(a)	Cscore^LB is the confidence score of predicted binding site. Cscore^LB values range in between [0-1]; where a higher score indicates a more reliable ligand-binding site prediction.
(b)	BS-score is a measure of local similarity (sequence & structure) between template binding site and predicted binding site in the query structure. Based on large scale benchmarking analysis, we have observed that a BS-score >1 reflects a significant local match between the predicted and template binding site.
(c)	TM-score is a measure of global structural similarity between query and template protein.
(d)	RMSD^a the RMSD between residues that are structurally aligned by TM-align.
(e)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(f)	Cov. represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

[Click result.zip to download all results on this page]

References:
1.	Wei Zheng, Qiqige Wuyun, Yang Li, Quancheng Liu, Xiaogen Zhou, Yiheng Zhu, P. Lydia Freddolino, Yang Zhang. Integrating deep learning potentials with I-TASSER for single- and multi-domain protein structure prediction. Submitted. 2023.