D-I-TASSER O60936

D-I-TASSER results for O60936

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

Summary of the Protein

Uniprot ID: O60936
Protein Name: Nucleolar protein 3
Gene Name: NOL3

Input Sequence in FASTA format

>O60936 (208 residues)
MGNAQERPSETIDRERKRLVETLQADSGLLLDALLARGVLTGPEYEALDALPDAERRVRR
LLLLVQGKGEAACQELLRCAQRTAGAPDPAWDWQHVGPGYRDRSYDPPCPGHWTPEAPGS
GTTCPGLPRASDPDEAGGPEGSEAVQSGTPEEPEPELEAEASKEAEPEPEPEPELEPEAE
AEPEPELEPEPDPEPEPDFEERDESEDS

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	O60936-D1	1-208	208		MGNAQERPSETIDRERKRLVETLQADSGLLLDALLARGVLTGPEYEALDALPDAERRVRRLLLLVQGKGEAACQELLRCAQRTAGAPDPAWDWQHVGPGYRDRSYDPPCPGHWTPEAPGSGTTCPGLPRASDPDEAGGPEGSEAVQSGTPEEPEPELEAEASKEAEPEPEPEPELEPEAEAEPEPELEPEPDPEPEPDFEERDESEDS

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.5269

(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	4m5dA	0.48	5.34	0.066	0.812	model1_4m5dA.pdb.gz
2	3agpA	0.48	5.57	0.060	0.817	model1_3agpA.pdb.gz
3	3mmpA	0.47	5.58	0.060	0.803	model1_3mmpA.pdb.gz
4	5dotA	0.47	5.98	0.029	0.851	model1_5dotA.pdb.gz
5	6mixA	0.46	5.06	0.047	0.755	model1_6mixA.pdb.gz
6	1z6tB	0.46	3.45	0.085	0.587	model1_1z6tB.pdb.gz
7	2a5yB	0.37	2.99	0.050	0.442	model1_2a5yB.pdb.gz
8	1vt4I1	0.37	2.84	0.058	0.447	model1_1vt4I1.pdb.gz
9	1jqmB	0.33	6.20	0.060	0.625	model1_1jqmB.pdb.gz
10	2mn4A	0.33	3.31	0.194	0.423	model1_2mn4A.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:0002020	0.75	protease binding
GO:0089720	0.74	caspase binding
GO:0046872	0.62	metal ion binding
GO:0005509	0.59	calcium ion binding
GO:0042802	0.55	identical protein binding
GO:0004857	0.55	enzyme inhibitor activity
GO:0043027	0.54	cysteine-type endopeptidase inhibitor activity involved in apoptotic process
GO:1901363	0.53	heterocyclic compound binding
GO:0097159	0.53	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:0065007	0.98	biological regulation
GO:0050794	0.94	regulation of cellular process
GO:0044699	0.88	single-organism process
GO:0009987	0.87	cellular process
GO:0048583	0.85	regulation of response to stimulus
GO:0023051	0.85	regulation of signaling
GO:0010646	0.85	regulation of cell communication
GO:1902531	0.84	regulation of intracellular signal transduction
GO:0044763	0.83	single-organism cellular process
GO:0065008	0.80	regulation of biological quality
GO:0080090	0.78	regulation of primary metabolic process
GO:0060255	0.78	regulation of macromolecule metabolic process
GO:0031323	0.78	regulation of cellular metabolic process
GO:0010468	0.77	regulation of gene expression
GO:0098771	0.76	inorganic ion homeostasis
GO:0030003	0.76	cellular cation homeostasis
GO:0048519	0.73	negative regulation of biological process
GO:0065009	0.72	regulation of molecular function
GO:0048523	0.72	negative regulation of cellular process
GO:0032268	0.72	regulation of cellular protein metabolic process
GO:2001233	0.71	regulation of apoptotic signaling pathway
GO:0080135	0.71	regulation of cellular response to stress
GO:0051129	0.71	negative regulation of cellular component organization
GO:0032879	0.71	regulation of localization
GO:0010951	0.71	negative regulation of endopeptidase activity
GO:0009968	0.71	negative regulation of signal transduction
GO:2001243	0.70	negative regulation of intrinsic apoptotic signaling pathway
GO:2001237	0.70	negative regulation of extrinsic apoptotic signaling pathway
GO:1903202	0.70	negative regulation of oxidative stress-induced cell death
GO:0097340	0.70	inhibition of cysteine-type endopeptidase activity
GO:0090201	0.70	negative regulation of release of cytochrome c from mitochondria
GO:0051480	0.70	regulation of cytosolic calcium ion concentration
GO:0051282	0.70	regulation of sequestering of calcium ion
GO:0043154	0.70	negative regulation of cysteine-type endopeptidase activity involved in apoptotic process
GO:0006810	0.58	transport
GO:0006811	0.56	ion transport
GO:0055085	0.54	transmembrane transport
GO:0016043	0.54	cellular component organization
GO:0098660	0.53	inorganic ion transmembrane transport
GO:0098662	0.51	inorganic cation transmembrane transport
GO:0072511	0.51	divalent inorganic cation transport
GO:0051649	0.51	establishment of localization in cell
GO:0051259	0.51	protein oligomerization
GO:0034622	0.51	cellular macromolecular complex assembly
GO:0030001	0.51	metal ion transport
GO:1990001	0.50	inhibition of cysteine-type endopeptidase activity involved in apoptotic process
GO:1902176	0.50	negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway
GO:0014808	0.50	release of sequestered calcium ion into cytosol by sarcoplasmic reticulum
GO:0006376	0.50	mRNA splice site selection

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	0.98	cell part
GO:0044424	0.93	intracellular part
GO:0005737	0.82	cytoplasm
GO:0043229	0.78	intracellular organelle
GO:0044444	0.77	cytoplasmic part
GO:0043227	0.77	membrane-bounded organelle
GO:0043231	0.76	intracellular membrane-bounded organelle
GO:0005739	0.69	mitochondrion

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	1hxgA	0.401	5.70	0.036	0.692	4.2.3.9 4.1.99.7	NA
2	0.060	2ffvA	0.368	5.89	0.062	0.668	2.4.1.41	151,155
3	0.060	1oqzB	0.396	5.51	0.027	0.668	3.5.1.93	NA
4	0.060	2zxqA	0.401	5.87	0.052	0.716	3.2.1.97	NA
5	0.060	1ea0A	0.395	5.71	0.042	0.697	1.4.1.13	65

	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	3puiA	0.418	5.49	0.090	0.707	0.98	NA	complex1.pdb.gz	130,131,134,139,140,142
2	0.01	2hcjB	0.288	5.67	0.031	0.500	0.58	GDP	complex2.pdb.gz	130,132,140,141,142
3	0.01	1efmA	0.248	5.06	0.028	0.389	0.43	GDP	complex3.pdb.gz	131,132,141,142

	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.