D-I-TASSER Q5D1E8

D-I-TASSER results for Q5D1E8

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

Summary of the Protein

Uniprot ID: Q5D1E8
Protein Name: Endoribonuclease ZC3H12A
Gene Name: ZC3H12A

Input Sequence in FASTA format

>Q5D1E8 (599 residues)
MSGPCGEKPVLEASPTMSLWEFEDSHSRQGTPRPGQELAAEEASALELQMKVDFFRKLGY
SSTEIHSVLQKLGVQADTNTVLGELVKHGTATERERQTSPDPCPQLPLVPRGGGTPKAPN
LEPPLPEEEKEGSDLRPVVIDGSNVAMSHGNKEVFSCRGILLAVNWFLERGHTDITVFVP
SWRKEQPRPDVPITDQHILRELEKKKILVFTPSRRVGGKRVVCYDDRFIVKLAYESDGIV
VSNDTYRDLQGERQEWKRFIEERLLMYSFVNDKFMPPDDPLGRHGPSLDNFLRKKPLTLE
HRKQPCPYGRKCTYGIKCRFFHPERPSCPQRSVADELRANALLSPPRAPSKDKNGRRPSP
SSQSSSLLTESEQCSLDGKKLGAQASPGSRQEGLTQTYAPSGRSLAPSGGSGSSFGPTDW
LPQTLDSLPYVSQDCLDSGIGSLESQMSELWGVRGGGPGEPGPPRAPYTGYSPYGSELPA
TAAFSAFGRAMGAGHFSVPADYPPAPPAFPPREYWSEPYPLPPPTSVLQEPPVQSPGAGR
SPWGRAGSLAKEQASVYTKLCGVFPPHLVEAVMGRFPQLLDPQQLAAEILSYKSQHPSE

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	Q5D1E8-D1	1-295	295		MSGPCGEKPVLEASPTMSLWEFEDSHSRQGTPRPGQELAAEEASALELQMKVDFFRKLGYSSTEIHSVLQKLGVQADTNTVLGELVKHGTATERERQTSPDPCPQLPLVPRGGGTPKAPNLEPPLPEEEKEGSDLRPVVIDGSNVAMSHGNKEVFSCRGILLAVNWFLERGHTDITVFVPSWRKEQPRPDVPITDQHILRELEKKKILVFTPSRRVGGKRVVCYDDRFIVKLAYESDGIVVSNDTYRDLQGERQEWKRFIEERLLMYSFVNDKFMPPDDPLGRHGPSLDNFLRKK
2	Q5D1E8-D2	296-599	304		PLTLEHRKQPCPYGRKCTYGIKCRFFHPERPSCPQRSVADELRANALLSPPRAPSKDKNGRRPSPSSQSSSLLTESEQCSLDGKKLGAQASPGSRQEGLTQTYAPSGRSLAPSGGSGSSFGPTDWLPQTLDSLPYVSQDCLDSGIGSLESQMSELWGVRGGGPGEPGPPRAPYTGYSPYGSELPATAAFSAFGRAMGAGHFSVPADYPPAPPAFPPREYWSEPYPLPPPTSVLQEPPVQSPGAGRSPWGRAGSLAKEQASVYTKLCGVFPPHLVEAVMGRFPQLLDPQQLAAEILSYKSQHPSE

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.51

(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	6cinA	0.36	7.96	0.040	0.599	model1_6cinA.pdb.gz
2	1kekA	0.36	8.00	0.038	0.598	model1_1kekA.pdb.gz
3	5dllA	0.36	7.60	0.039	0.564	model1_5dllA.pdb.gz
4	6w2jA	0.35	7.95	0.041	0.588	model1_6w2jA.pdb.gz
5	3ir7A	0.35	7.70	0.026	0.564	model1_3ir7A.pdb.gz
6	7edxB	0.35	7.80	0.033	0.568	model1_7edxB.pdb.gz
7	3c68A	0.35	8.05	0.038	0.579	model1_3c68A.pdb.gz
8	2dqmA	0.35	7.81	0.043	0.564	model1_2dqmA.pdb.gz
9	6oiuA	0.35	7.78	0.040	0.566	model1_6oiuA.pdb.gz
10	6d2wA	0.35	7.60	0.050	0.551	model1_6d2wA.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:1901363	0.88	heterocyclic compound binding
GO:0097159	0.88	organic cyclic compound binding
GO:0044822	0.87	poly(A) RNA binding
GO:0003824	0.87	catalytic activity
GO:0004532	0.86	exoribonuclease activity
GO:0003729	0.86	mRNA binding
GO:0003682	0.86	chromatin binding
GO:0003677	0.86	DNA binding
GO:0035925	0.85	mRNA 3'-UTR AU-rich region binding
GO:0035613	0.85	RNA stem-loop binding
GO:0035198	0.85	miRNA binding
GO:0004521	0.85	endoribonuclease activity
GO:0004843	0.65	thiol-dependent ubiquitin-specific protease 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:0032269	1.00	negative regulation of cellular protein metabolic process
GO:0031329	0.88	regulation of cellular catabolic process
GO:0009987	0.88	cellular process
GO:2000112	0.83	regulation of cellular macromolecule biosynthetic process
GO:0051171	0.83	regulation of nitrogen compound metabolic process
GO:0010468	0.83	regulation of gene expression
GO:0061158	0.82	3'-UTR-mediated mRNA destabilization
GO:0008152	0.80	metabolic process
GO:0044260	0.79	cellular macromolecule metabolic process
GO:0044238	0.79	primary metabolic process
GO:0016070	0.78	RNA metabolic process
GO:0050896	0.77	response to stimulus
GO:0051716	0.76	cellular response to stimulus
GO:0048518	0.76	positive regulation of biological process
GO:0048522	0.74	positive regulation of cellular process
GO:0051239	0.73	regulation of multicellular organismal process
GO:0048583	0.73	regulation of response to stimulus
GO:2000026	0.72	regulation of multicellular organismal development
GO:0080134	0.72	regulation of response to stress
GO:0031399	0.72	regulation of protein modification process
GO:0031325	0.72	positive regulation of cellular metabolic process
GO:0030162	0.72	regulation of proteolysis
GO:0010604	0.72	positive regulation of macromolecule metabolic process
GO:1903320	0.71	regulation of protein modification by small protein conjugation or removal
GO:1902531	0.71	regulation of intracellular signal transduction
GO:0051241	0.71	negative regulation of multicellular organismal process
GO:0051240	0.71	positive regulation of multicellular organismal process
GO:0048585	0.71	negative regulation of response to stimulus
GO:0045893	0.71	positive regulation of transcription, DNA-templated
GO:0045765	0.71	regulation of angiogenesis
GO:0045595	0.71	regulation of cell differentiation
GO:0042981	0.71	regulation of apoptotic process
GO:0032879	0.71	regulation of localization
GO:0032270	0.71	positive regulation of cellular protein metabolic process
GO:0031347	0.71	regulation of defense response
GO:0016043	0.71	cellular component organization
GO:0001817	0.71	regulation of cytokine production
GO:2000627	0.70	positive regulation of miRNA catabolic process
GO:1990869	0.70	cellular response to chemokine
GO:1904637	0.70	cellular response to ionomycin
GO:1904628	0.70	cellular response to phorbol 13-acetate 12-myristate
GO:1904468	0.70	negative regulation of tumor necrosis factor secretion
GO:1903799	0.70	negative regulation of production of miRNAs involved in gene silencing by miRNA
GO:1902714	0.70	negative regulation of interferon-gamma secretion
GO:1900165	0.70	negative regulation of interleukin-6 secretion
GO:1900016	0.70	negative regulation of cytokine production involved in inflammatory response
GO:0090502	0.70	RNA phosphodiester bond hydrolysis, endonucleolytic
GO:0071356	0.70	cellular response to tumor necrosis factor
GO:0071222	0.70	cellular response to lipopolysaccharide
GO:0061014	0.70	positive regulation of mRNA catabolic process
GO:0055118	0.70	negative regulation of cardiac muscle contraction
GO:0051259	0.70	protein oligomerization
GO:0050713	0.70	negative regulation of interleukin-1 beta secretion
GO:0045944	0.70	positive regulation of transcription from RNA polymerase II promoter
GO:0045766	0.70	positive regulation of angiogenesis
GO:0045600	0.70	positive regulation of fat cell differentiation
GO:0045019	0.70	negative regulation of nitric oxide biosynthetic process
GO:0042347	0.70	negative regulation of NF-kappaB import into nucleus
GO:0010942	0.70	positive regulation of cell death
GO:0010656	0.70	negative regulation of muscle cell apoptotic process
GO:0010595	0.70	positive regulation of endothelial cell migration
GO:0031400	0.55	negative regulation of protein modification process
GO:0045862	0.54	positive regulation of proteolysis
GO:0006950	0.54	response to stress
GO:1903003	0.53	positive regulation of protein deubiquitination
GO:0044699	0.53	single-organism process
GO:0006974	0.53	cellular response to DNA damage stimulus

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:0043232	1.00	intracellular non-membrane-bounded organelle
GO:0044446	0.90	intracellular organelle part
GO:0044444	0.88	cytoplasmic part
GO:0032991	0.85	macromolecular complex
GO:0043231	0.83	intracellular membrane-bounded organelle
GO:0030529	0.83	intracellular ribonucleoprotein complex
GO:0005737	0.82	cytoplasm
GO:0005634	0.82	nucleus
GO:0000932	0.82	cytoplasmic mRNA processing body
GO:0044425	0.74	membrane part
GO:0044432	0.71	endoplasmic reticulum part
GO:0042406	0.70	extrinsic component of endoplasmic reticulum membrane
GO:0005856	0.70	cytoskeleton
GO:0005791	0.70	rough endoplasmic reticulum
GO:0044428	0.57	nuclear part
GO:0043234	0.56	protein complex

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	2pffA	0.324	8.00	0.023	0.531	2.3.1.41 2.3.1.86	NA
2	0.060	2j5wA	0.328	8.09	0.031	0.553	1.16.3.1	NA
3	0.060	1br2A	0.287	7.92	0.042	0.469	3.6.1.32	NA
4	0.060	3ebgA	0.344	7.68	0.060	0.548	3.4.11.-	NA
5	0.060	1l5jA	0.322	8.10	0.027	0.539	4.2.1.3	160

	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	1siwA	0.356	7.90	0.029	0.578	0.52	SF4	complex1.pdb.gz	144,150,156,157,159
2	0.01	1ce8G	0.337	8.08	0.030	0.561	0.42	IMP	complex2.pdb.gz	142,145,178,228,242
3	0.01	1a9x1	0.372	7.86	0.047	0.603	0.46	III	complex3.pdb.gz	143,146,161,162
4	0.01	2c3oA	0.359	8.05	0.036	0.601	0.41	SF4	complex4.pdb.gz	149,150,151,152,153,192,193,194
5	0.01	1b0pA	0.358	8.00	0.040	0.601	0.42	SF4	complex5.pdb.gz	139,145,146,160,161,163,177
6	0.01	1b0pA	0.358	8.00	0.040	0.601	0.49	SF4	complex6.pdb.gz	146,147,159,160,179
7	0.01	1ce8A	0.336	8.16	0.036	0.571	0.44	IMP	complex7.pdb.gz	143,156,157,160,179,180,181,198,199

	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.