D-I-TASSER P02708

D-I-TASSER results for P02708

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

Summary of the Protein

Uniprot ID: P02708
Protein Name: Acetylcholine receptor subunit alpha
Gene Name: CHRNA1

Input Sequence in FASTA format

>P02708 (482 residues)
MEPWPLLLLFSLCSAGLVLGSEHETRLVAKLFKDYSSVVRPVEDHRQVVEVTVGLQLIQL
INVDEVNQIVTTNVRLKQGDMVDLPRPSCVTLGVPLFSHLQNEQWVDYNLKWNPDDYGGV
KKIHIPSEKIWRPDLVLYNNADGDFAIVKFTKVLLQYTGHITWTPPAIFKSYCEIIVTHF
PFDEQNCSMKLGTWTYDGSVVAINPESDQPDLSNFMESGEWVIKESRGWKHSVTYSCCPD
TPYLDITYHFVMQRLPLYFIVNVIIPCLLFSFLTGLVFYLPTDSGEKMTLSISVLLSLTV
FLLVIVELIPSTSSAVPLIGKYMLFTMVFVIASIIITVIVINTHHRSPSTHVMPNWVRKV
FIDTIPNIMFFSTMKRPSREKQDKKIFTEDIDISDISGKPGPPPMGFHSPLIKHPEVKSA
IEGIKYIAETMKSDQESNNAAAEWKYVAMVMDHILLGVFMLVCIIGTLAVFAGRLIELNQ
QG

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 AttentionPotential. 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	P02708-D1	1-482	482		MEPWPLLLLFSLCSAGLVLGSEHETRLVAKLFKDYSSVVRPVEDHRQVVEVTVGLQLIQLINVDEVNQIVTTNVRLKQGDMVDLPRPSCVTLGVPLFSHLQNEQWVDYNLKWNPDDYGGVKKIHIPSEKIWRPDLVLYNNADGDFAIVKFTKVLLQYTGHITWTPPAIFKSYCEIIVTHFPFDEQNCSMKLGTWTYDGSVVAINPESDQPDLSNFMESGEWVIKESRGWKHSVTYSCCPDTPYLDITYHFVMQRLPLYFIVNVIIPCLLFSFLTGLVFYLPTDSGEKMTLSISVLLSLTVFLLVIVELIPSTSSAVPLIGKYMLFTMVFVIASIIITVIVINTHHRSPSTHVMPNWVRKVFIDTIPNIMFFSTMKRPSREKQDKKIFTEDIDISDISGKPGPPPMGFHSPLIKHPEVKSAIEGIKYIAETMKSDQESNNAAAEWKYVAMVMDHILLGVFMLVCIIGTLAVFAGRLIELNQQG

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.7287

(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 AttentionPotential, 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	6pv7A	0.79	1.06	0.553	0.803	model1_6pv7A.pdb.gz
2	7kooA	0.75	2.29	0.388	0.807	model1_7kooA.pdb.gz
3	5kxiA	0.73	1.61	0.526	0.753	model1_5kxiA.pdb.gz
4	5kxiB	0.71	1.59	0.463	0.739	model1_5kxiB.pdb.gz
5	4pirA	0.71	2.81	0.245	0.786	model1_4pirA.pdb.gz
6	2bg9E	0.66	3.38	0.275	0.755	model1_2bg9E.pdb.gz
7	2bg9A	0.66	3.39	0.486	0.755	model1_2bg9A.pdb.gz
8	2bg9B	0.65	3.46	0.285	0.749	model1_2bg9B.pdb.gz
9	2bg9C	0.65	3.37	0.268	0.749	model1_2bg9C.pdb.gz
10	4cofA	0.63	2.58	0.202	0.680	model1_4cofA.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:0099600	0.98	transmembrane receptor activity
GO:0004888	0.91	transmembrane signaling receptor activity
GO:0022857	0.90	transmembrane transporter activity
GO:0005216	0.89	ion channel activity
GO:0005230	0.87	extracellular ligand-gated ion channel activity
GO:0005231	0.86	excitatory extracellular ligand-gated ion channel activity
GO:0043167	0.82	ion binding
GO:0004889	0.81	acetylcholine-activated cation-selective channel activity
GO:0030594	0.80	neurotransmitter receptor activity
GO:0043169	0.79	cation binding
GO:0015464	0.79	acetylcholine receptor activity
GO:0042166	0.76	acetylcholine 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	0.99	single-organism process
GO:0044763	0.98	single-organism cellular process
GO:0007268	0.96	chemical synaptic transmission
GO:0007271	0.91	synaptic transmission, cholinergic
GO:0050896	0.65	response to stimulus
GO:0042221	0.62	response to chemical
GO:0006810	0.61	transport
GO:0010033	0.60	response to organic substance
GO:0009719	0.60	response to endogenous stimulus
GO:0010243	0.59	response to organonitrogen compound
GO:0006811	0.58	ion transport
GO:0014070	0.55	response to organic cyclic compound
GO:0035094	0.54	response to nicotine
GO:0007274	0.54	neuromuscular synaptic transmission
GO:0006812	0.54	cation transport
GO:0065007	0.53	biological regulation
GO:0055085	0.51	transmembrane transport
GO:0034220	0.50	ion transmembrane transport

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	0.97	cell part
GO:0043234	0.93	protein complex
GO:0043235	0.92	receptor complex
GO:0044425	0.85	membrane part
GO:0044459	0.84	plasma membrane part
GO:0098797	0.82	plasma membrane protein complex
GO:0005892	0.81	acetylcholine-gated channel complex
GO:0044424	0.51	intracellular part

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	2vz8A	0.330	7.31	0.044	0.535	2.3.1.85	NA
2	0.060	1kv3A	0.243	7.55	0.042	0.415	2.3.2.13	NA
3	0.060	1ej6A	0.313	7.65	0.050	0.535	2.7.7.50	NA
4	0.060	2dewX	0.311	6.88	0.045	0.475	3.5.3.15	NA
5	0.060	3b8cA	0.310	7.20	0.052	0.504	3.6.3.6	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	0.09	3p4wD	0.586	2.67	0.165	0.643	0.22	DSF	complex1.pdb.gz	28,119,120
2	0.09	3sioA	0.411	2.64	0.215	0.444	0.34	MLK	complex2.pdb.gz	30,120,156,157
3	0.07	2bysB	0.402	2.23	0.228	0.427	0.32	LOB	complex3.pdb.gz	115,117,118,157,159
4	0.06	3sh1C	0.412	2.77	0.208	0.448	0.20	MLK	complex4.pdb.gz	32,117,158
5	0.04	3sh1D	0.409	2.62	0.206	0.442	0.17	MLK	complex5.pdb.gz	30,117,118
6	0.03	3sh1B	0.410	2.68	0.206	0.444	0.19	MLK	complex6.pdb.gz	30,121,157
7	0.02	2uz6G	0.395	2.57	0.224	0.425	0.28	III	complex7.pdb.gz	30,120,155
8	0.02	2c9tA	0.394	2.50	0.221	0.423	0.20	III	complex8.pdb.gz	30,120,159

	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, Chengxin Zhang, Yang Li, Robin Pearce, Eric W. Bell, Yang Zhang. Folding non-homology proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. In preparation, 2020.