D-I-TASSER P02786

D-I-TASSER results for P02786

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

Summary of the Protein

Uniprot ID: P02786
Protein Name: Transferrin receptor protein 1
Gene Name: TFRC

Input Sequence in FASTA format

>P02786 (760 residues)
MMDQARSAFSNLFGGEPLSYTRFSLARQVDGDNSHVEMKLAVDEEENADNNTKANVTKPK
RCSGSICYGTIAVIVFFLIGFMIGYLGYCKGVEPKTECERLAGTESPVREEPGEDFPAAR
RLYWDDLKRKLSEKLDSTDFTGTIKLLNENSYVPREAGSQKDENLALYVENQFREFKLSK
VWRDQHFVKIQVKDSAQNSVIIVDKNGRLVYLVENPGGYVAYSKAATVTGKLVHANFGTK
KDFEDLYTPVNGSIVIVRAGKITFAEKVANAESLNAIGVLIYMDQTKFPIVNAELSFFGH
AHLGTGDPYTPGFPSFNHTQFPPSRSSGLPNIPVQTISRAAAEKLFGNMEGDCPSDWKTD
STCRMVTSESKNVKLTVSNVLKEIKILNIFGVIKGFVEPDHYVVVGAQRDAWGPGAAKSG
VGTALLLKLAQMFSDMVLKDGFQPSRSIIFASWSAGDFGSVGATEWLEGYLSSLHLKAFT
YINLDKAVLGTSNFKVSASPLLYTLIEKTMQNVKHPVTGQFLYQDSNWASKVEKLTLDNA
AFPFLAYSGIPAVSFCFCEDTDYPYLGTTMDTYKELIERIPELNKVARAAAEVAGQFVIK
LTHDVELNLDYERYNSQLLSFVRDLNQYRADIKEMGLSLQWLYSARGDFFRATSRLTTDF
GNAEKTDRFVMKKLNDRVMRVEYHFLSPYVSPKESPFRHVFWGSGSHTLPALLENLKLRK
QNNGAFNETLFRNQLALATWTIQGAANALSGDVWDIDNEF

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	P02786-D1	1-536,552-608	593		MMDQARSAFSNLFGGEPLSYTRFSLARQVDGDNSHVEMKLAVDEEENADNNTKANVTKPKRCSGSICYGTIAVIVFFLIGFMIGYLGYCKGVEPKTECERLAGTESPVREEPGEDFPAARRLYWDDLKRKLSEKLDSTDFTGTIKLLNENSYVPREAGSQKDENLALYVENQFREFKLSKVWRDQHFVKIQVKDSAQNSVIIVDKNGRLVYLVENPGGYVAYSKAATVTGKLVHANFGTKKDFEDLYTPVNGSIVIVRAGKITFAEKVANAESLNAIGVLIYMDQTKFPIVNAELSFFGHAHLGTGDPYTPGFPSFNHTQFPPSRSSGLPNIPVQTISRAAAEKLFGNMEGDCPSDWKTDSTCRMVTSESKNVKLTVSNVLKEIKILNIFGVIKGFVEPDHYVVVGAQRDAWGPGAAKSGVGTALLLKLAQMFSDMVLKDGFQPSRSIIFASWSAGDFGSVGATEWLEGYLSSLHLKAFTYINLDKAVLGTSNFKVSASPLLYTLIEKTMQNVKHPVTGQFLYQDSNWASKVEKLTAVSFCFCEDTDYPYLGTTMDTYKELIERIPELNKVARAAAEVAGQFVIKLTHDVELN
2	P02786-D2	537-551,609-760	167		LDNAAFPFLAYSGIPLDYERYNSQLLSFVRDLNQYRADIKEMGLSLQWLYSARGDFFRATSRLTTDFGNAEKTDRFVMKKLNDRVMRVEYHFLSPYVSPKESPFRHVFWGSGSHTLPALLENLKLRKQNNGAFNETLFRNQLALATWTIQGAANALSGDVWDIDNEF

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.82

(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	4tweA	0.76	3.29	0.234	0.825	model1_4tweA.pdb.gz
2	1z8lA	0.75	3.10	0.224	0.810	model1_1z8lA.pdb.gz
3	1suvA	0.74	3.44	0.935	0.822	model1_1suvA.pdb.gz
4	3iibA	0.49	3.51	0.167	0.543	model1_3iibA.pdb.gz
5	6hc6A	0.46	3.19	0.188	0.508	model1_6hc6A.pdb.gz
6	2ek8A	0.46	3.69	0.168	0.517	model1_2ek8A.pdb.gz
7	3k9tA	0.37	4.73	0.084	0.442	model1_3k9tA.pdb.gz
8	3eifA	0.34	7.29	0.071	0.488	model1_3eifA.pdb.gz
9	3b35A	0.33	2.54	0.177	0.347	model1_3b35A.pdb.gz
10	1tkjA	0.31	2.47	0.151	0.332	model1_1tkjA.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:0022857	0.74	transmembrane transporter activity
GO:0022890	0.73	inorganic cation transmembrane transporter activity
GO:0046873	0.72	metal ion transmembrane transporter activity
GO:0015405	0.72	P-P-bond-hydrolysis-driven transmembrane transporter activity
GO:0033570	0.71	transferrin transmembrane transporter 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 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:0009987	0.92	cellular process
GO:0044699	0.91	single-organism process
GO:0008152	0.91	metabolic process
GO:0071704	0.90	organic substance metabolic process
GO:0065007	0.90	biological regulation
GO:0043170	0.89	macromolecule metabolic process
GO:0044763	0.87	single-organism cellular process
GO:0044237	0.84	cellular metabolic process
GO:0044260	0.78	cellular macromolecule metabolic process
GO:0050789	0.75	regulation of biological process
GO:0050794	0.72	regulation of cellular process
GO:0006810	0.68	transport
GO:0048518	0.67	positive regulation of biological process
GO:0048522	0.66	positive regulation of cellular process
GO:0015031	0.65	protein transport
GO:0080090	0.64	regulation of primary metabolic process
GO:0060255	0.64	regulation of macromolecule metabolic process
GO:0031323	0.64	regulation of cellular metabolic process
GO:0044710	0.63	single-organism metabolic process
GO:0031325	0.63	positive regulation of cellular metabolic process
GO:0019219	0.63	regulation of nucleobase-containing compound metabolic process
GO:0010604	0.63	positive regulation of macromolecule metabolic process
GO:0045935	0.62	positive regulation of nucleobase-containing compound metabolic process
GO:0033572	0.62	transferrin transport
GO:0006897	0.62	endocytosis
GO:0006898	0.61	receptor-mediated endocytosis
GO:0051239	0.58	regulation of multicellular organismal process
GO:2000026	0.57	regulation of multicellular organismal development
GO:0048583	0.57	regulation of response to stimulus
GO:0051240	0.56	positive regulation of multicellular organismal process
GO:0051094	0.56	positive regulation of developmental process
GO:0050778	0.56	positive regulation of immune response
GO:0042127	0.56	regulation of cell proliferation
GO:0030155	0.56	regulation of cell adhesion
GO:0045830	0.55	positive regulation of isotype switching
GO:0042102	0.55	positive regulation of T cell proliferation
GO:0031623	0.55	receptor internalization
GO:0030890	0.55	positive regulation of B cell proliferation

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:0044424	0.90	intracellular part
GO:0043227	0.86	membrane-bounded organelle
GO:0044444	0.78	cytoplasmic part
GO:0043229	0.72	intracellular organelle
GO:0043231	0.71	intracellular membrane-bounded organelle
GO:0044425	0.64	membrane part
GO:0016021	0.61	integral component of membrane
GO:0016020	0.57	membrane
GO:0031982	0.53	vesicle

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	0.165	1z8lA	0.750	3.10	0.224	0.810	3.4.17.21	NA
2	0.060	3c46B	0.309	8.16	0.039	0.480	2.7.7.6	468
3	0.060	1n1hA	0.324	8.96	0.030	0.551	2.7.7.48	NA
4	0.060	1ahpA	0.311	8.01	0.039	0.479	2.4.1.1	NA
5	0.060	3l4uA	0.297	8.29	0.049	0.471	3.2.1.20 3.2.1.3	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	0.15	3bxmA	0.750	3.11	0.232	0.810	0.53	III	complex1.pdb.gz	418,457,459,485,486
2	0.15	3d7gA	0.750	3.12	0.232	0.810	0.46	MUD	complex2.pdb.gz	456,457,459,460
3	0.13	1de40	0.740	3.35	0.907	0.813	1.09	III	complex3.pdb.gz	180,182,312,314,316,317,320,392,394,399,400,402,447,449,469,471,472,473,474,475,476
4	0.04	2xeiA	0.750	3.10	0.232	0.810	0.42	ARK	complex4.pdb.gz	456,457,459,566,567
5	0.04	1z8l0	0.750	3.10	0.224	0.810	0.47	III	complex5.pdb.gz	313,314,397,399,400,447,469,472,476,477

	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.