D-I-TASSER P09603

D-I-TASSER results for P09603

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

Summary of the Protein

Uniprot ID: P09603
Protein Name: Macrophage colony-stimulating factor 1
Gene Name: CSF1

Input Sequence in FASTA format

>P09603 (554 residues)
MTAPGAAGRCPPTTWLGSLLLLVCLLASRSITEEVSEYCSHMIGSGHLQSLQRLIDSQME
TSCQITFEFVDQEQLKDPVCYLKKAFLLVQDIMEDTMRFRDNTPNAIAIVQLQELSLRLK
SCFTKDYEEHDKACVRTFYETPLQLLEKVKNVFNETKNLLDKDWNIFSKNCNNSFAECSS
QDVVTKPDCNCLYPKAIPSSDPASVSPHQPLAPSMAPVAGLTWEDSEGTEGSSLLPGEQP
LHTVDPGSAKQRPPRSTCQSFEPPETPVVKDSTIGGSPQPRPSVGAFNPGMEDILDSAMG
TNWVPEEASGEASEIPVPQGTELSPSRPGGGSMQTEPARPSNFLSASSPLPASAKGQQPA
DVTGTALPRVGPVRPTGQDWNHTPQKTDHPSALLRDPPEPGSPRISSLRPQGLSNPSTLS
AQPQLSRSHSSGSVLPLGELEGRRSTRDRRSPAEPEGGPASEGAARPLPRFNSVPLTDTG
HERQSEGSFSPQLQESVFHLLVPSVILVLLAVGGLLFYRWRRRSHQEPQRADSPLEQPEG
SPLTQDDRQVELPV

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	P09603-D1	1-181	181		MTAPGAAGRCPPTTWLGSLLLLVCLLASRSITEEVSEYCSHMIGSGHLQSLQRLIDSQMETSCQITFEFVDQEQLKDPVCYLKKAFLLVQDIMEDTMRFRDNTPNAIAIVQLQELSLRLKSCFTKDYEEHDKACVRTFYETPLQLLEKVKNVFNETKNLLDKDWNIFSKNCNNSFAECSSQ
2	P09603-D2	182-483	302		DVVTKPDCNCLYPKAIPSSDPASVSPHQPLAPSMAPVAGLTWEDSEGTEGSSLLPGEQPLHTVDPGSAKQRPPRSTCQSFEPPETPVVKDSTIGGSPQPRPSVGAFNPGMEDILDSAMGTNWVPEEASGEASEIPVPQGTELSPSRPGGGSMQTEPARPSNFLSASSPLPASAKGQQPADVTGTALPRVGPVRPTGQDWNHTPQKTDHPSALLRDPPEPGSPRISSLRPQGLSNPSTLSAQPQLSRSHSSGSVLPLGELEGRRSTRDRRSPAEPEGGPASEGAARPLPRFNSVPLTDTGHER
3	P09603-D3	484-554	71		QSEGSFSPQLQESVFHLLVPSVILVLLAVGGLLFYRWRRRSHQEPQRADSPLEQPEGSPLTQDDRQVELPV

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.46

(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	5h3zA	0.37	7.91	0.033	0.626	model1_5h3zA.pdb.gz
2	1t0rA	0.36	6.90	0.051	0.538	model1_1t0rA.pdb.gz
3	5fauA	0.36	7.69	0.041	0.581	model1_5fauA.pdb.gz
4	2f3oA	0.36	7.75	0.040	0.585	model1_2f3oA.pdb.gz
5	6r9tA	0.36	7.79	0.052	0.576	model1_6r9tA.pdb.gz
6	6xs4A	0.36	7.80	0.052	0.588	model1_6xs4A.pdb.gz
7	3dhiA	0.36	6.98	0.063	0.536	model1_3dhiA.pdb.gz
8	6lonB	0.36	7.61	0.040	0.570	model1_6lonB.pdb.gz
9	3cmuA	0.35	7.74	0.047	0.581	model1_3cmuA.pdb.gz
10	1mhzD	0.35	6.96	0.043	0.529	model1_1mhzD.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:0042803	0.91	protein homodimerization activity
GO:0005102	0.75	receptor binding
GO:0005125	0.69	cytokine activity
GO:0005126	0.68	cytokine receptor binding
GO:0008083	0.66	growth factor activity
GO:0005157	0.66	macrophage colony-stimulating factor receptor 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	0.98	single-organism process
GO:0009987	0.98	cellular process
GO:0044767	0.97	single-organism developmental process
GO:0030316	0.97	osteoclast differentiation
GO:0008283	0.97	cell proliferation
GO:0065007	0.87	biological regulation
GO:0050789	0.86	regulation of biological process
GO:0050794	0.84	regulation of cellular process
GO:0048518	0.79	positive regulation of biological process
GO:0048522	0.78	positive regulation of cellular process
GO:0051240	0.75	positive regulation of multicellular organismal process
GO:0031323	0.75	regulation of cellular metabolic process
GO:2000026	0.74	regulation of multicellular organismal development
GO:0080090	0.74	regulation of primary metabolic process
GO:0060255	0.74	regulation of macromolecule metabolic process
GO:0051094	0.74	positive regulation of developmental process
GO:0045597	0.74	positive regulation of cell differentiation
GO:0009893	0.74	positive regulation of metabolic process
GO:0002684	0.74	positive regulation of immune system process
GO:0048583	0.73	regulation of response to stimulus
GO:0045651	0.73	positive regulation of macrophage differentiation
GO:0032268	0.73	regulation of cellular protein metabolic process
GO:0031325	0.73	positive regulation of cellular metabolic process
GO:0019220	0.73	regulation of phosphate metabolic process
GO:0010604	0.73	positive regulation of macromolecule metabolic process
GO:0048584	0.72	positive regulation of response to stimulus
GO:0009966	0.72	regulation of signal transduction
GO:0007165	0.72	signal transduction
GO:0001934	0.72	positive regulation of protein phosphorylation
GO:0048856	0.71	anatomical structure development
GO:0032879	0.71	regulation of localization
GO:0010628	0.71	positive regulation of gene expression
GO:0009967	0.71	positive regulation of signal transduction
GO:0007166	0.71	cell surface receptor signaling pathway
GO:1904141	0.70	positive regulation of microglial cell migration
GO:1902228	0.70	positive regulation of macrophage colony-stimulating factor signaling pathway
GO:0045860	0.70	positive regulation of protein kinase activity
GO:0045672	0.70	positive regulation of osteoclast differentiation
GO:0045657	0.70	positive regulation of monocyte differentiation
GO:0032946	0.70	positive regulation of mononuclear cell proliferation
GO:0010759	0.70	positive regulation of macrophage chemotaxis
GO:0010744	0.70	positive regulation of macrophage derived foam cell differentiation
GO:0007169	0.70	transmembrane receptor protein tyrosine kinase signaling pathway
GO:0003006	0.70	developmental process involved in reproduction
GO:0001954	0.70	positive regulation of cell-matrix adhesion
GO:0030225	0.68	macrophage differentiation
GO:0032501	0.57	multicellular organismal process
GO:0009653	0.57	anatomical structure morphogenesis
GO:0044707	0.56	single-multicellular organism process

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:0005615	1.00	extracellular space
GO:0044464	0.89	cell part
GO:0044424	0.84	intracellular part
GO:0044444	0.77	cytoplasmic part
GO:0043226	0.76	organelle
GO:0043227	0.75	membrane-bounded organelle
GO:0032991	0.74	macromolecular complex
GO:0043234	0.73	protein complex
GO:1990682	0.70	CSF1-CSF1R complex
GO:0070062	0.70	extracellular exosome
GO:0048471	0.70	perinuclear region of cytoplasm
GO:0016020	0.51	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	1e1yA	0.316	8.20	0.038	0.549	2.4.1.1	NA
2	0.060	1mhyD	0.350	6.73	0.048	0.520	1.14.13.25	122,156
3	0.060	1fa9A	0.316	8.02	0.033	0.540	2.4.1.1	NA
4	0.060	1clqA	0.282	7.63	0.037	0.453	2.7.7.7	244
5	0.060	1ynnJ	0.174	6.44	0.034	0.255	2.7.7.6	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:

Click to view	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	2avu2	0.075	2.81	0.033	0.081	0.11	III	complex1.pdb.gz	153,520,543

	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.