ASpdb: an integrative knowledgebase of human protein isoforms from experimental and AI-predicted structures

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	Protein Summary
	AS Summary
	Protein Functional Features
	Gene Isoform Structures and Expression Levels
	Protein Structures
	pLDDT Score Distribution
	Ramachandran Plot of Protein Structures
	Potential Active Site Information
	Protein Structure and Feature Comparision
	Protein-Protein Interaction
	Related Drugs
	Related Diseases
	Clinically Important Variants

Protein:ERG

Protein Summary

Gene summary

Gene name: ERG
ASpdb.0 ID: 2078
	Gene
Gene symbol	ERG
Gene ID	2078
Gene name	ETS transcription factor ERG
Synonyms	LMPHM14\|erg-3\|p55
Cytomap	21q22.2
Type of gene	protein-coding
Description	transcriptional regulator ERGERG, ETS transcription factorFUS/ERG fusion proteinTMPRSS2/ERG fusionets-relatedtranscriptional regulator ERG (transforming protein ERG)v-ets avian erythroblastosis virus E26 oncogene homologv-ets avian erythroblastosis
Modification date	20240323
UniProtAcc	P11308

Gene ontology of this gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner	Gene	GO ID	GO term	PubMed ID
Gene	ERG	GO:0000978	RNA polymerase II cis-regulatory region sequence-specific DNA binding	23093599
Gene	ERG	GO:0005654	nucleoplasm	-
Gene	ERG	GO:0005829	cytosol	-
Gene	ERG	GO:0045944	positive regulation of transcription by RNA polymerase II	18195090\|23913826
Gene	ERG	GO:1990837	sequence-specific double-stranded DNA binding	28473536
Gene	ERG	GO:1990904	ribonucleoprotein complex	17289661

AS Summary

Information of the canonical protein with experimentally identified structure from PDB (2023).

UniProt Acc	File name	PDB ID	Method	Resolution	Chain	Start	End
P11308-4	P11308-4_4irh_A.pdb	4IRH	X-ray	2.1	A	300	401

ASpdb's canonical and alternatively spliced isoform information.

accession_id	gene_name	canonical_id	alternative_id	canonical_length	alternative_length	canonical_start	canonical_end	type	originalSEQ	variationSEQ	alternative_start	alternative_end
P11308	ERG	P11308-4	P11308-1	479	462	1	4	Substitution	MAST	MIQTVPDPAAH	1	11
P11308	ERG	P11308-4	P11308-1	479	462	225	248	Deletion	none	none	231	231
P11308	ERG	P11308-4	P11308-2	479	363	1	92	Deletion	none	none	0	0
P11308	ERG	P11308-4	P11308-2	479	363	225	248	Deletion	none	none	132	132
P11308	ERG	P11308-4	P11308-3	479	486	1	4	Substitution	MAST	MIQTVPDPAAH	1	11
P11308	ERG	P11308-4	P11308-5	479	317	1	4	Substitution	MAST	MIQTVPDPAAH	1	11
P11308	ERG	P11308-4	P11308-5	479	317	308	310	Substitution	SGQ	WTQ	315	317
P11308	ERG	P11308-4	P11308-5	479	317	311	479	Deletion	none	none	317	317
P11308	ERG	P11308-4	P11308-6	479	325	1	4	Substitution	MAST	MIQTVPDPAAH	1	11
P11308	ERG	P11308-4	P11308-6	479	325	249	318	Substitution	DLPYEPPRRSAWTGHGHPTPQSKAAQPSPSTVPKTEDQRPQLDPYQILGPTSSRLANPGSGQIQLWQFLL	GTKTPLCDLFIERHPRCPAEIRALSHVIQRELIPELKPVPDSLILPLLIWRLNPLKPFHSKTTLKELRAD	256	325
P11308	ERG	P11308-4	P11308-6	479	325	319	479	Deletion	none	none	325	325

Multiple sequence alignment of our canonical and alternatively spliced ERG

Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of ERG

UniProt-id	ENSG	ENST	ENSP
P11308-4	ENSG00000157554.20	ENST00000288319.12	ENSP00000288319.7
P11308-1	ENSG00000157554.20	ENST00000398911.5	ENSP00000381882.1
P11308-1	ENSG00000157554.20	ENST00000442448.5	ENSP00000394694.1
P11308-2	ENSG00000157554.20	ENST00000398897.5	ENSP00000381871.1
P11308-3	ENSG00000157554.20	ENST00000398919.6	ENSP00000381891.2
P11308-3	ENSG00000157554.20	ENST00000417133.6	ENSP00000414150.2

UniProt-id	NM ID	NP ID
P11308-4	NM_182918.3	NP_891548.1
P11308-1	NM_004449.4	NP_004440.1
P11308-2	NM_001243429.1	NP_001230358.1
P11308-3	NM_001136154.1	NP_001129626.1
P11308-3	NM_001243428.1	NP_001230357.1
P11308-5	NM_001243432.2	NP_001230361.1
P11308-6	NM_001291391.1	NP_001278320.1

Amino acid sequences of our canonical and alternatively spliced ERG

accession_id	Protein sequence
P11308-4	MASTIKEALSVVSEDQSLFECAYGTPHLAKTEMTASSSSDYGQTSKMSPRVPQQDWLSQPPARVTIKMECNPSQVNGSRNSPDECSVAKG GKMVGSPDTVGMNYGSYMEEKHMPPPNMTTNERRVIVPADPTLWSTDHVRQWLEWAVKEYGLPDVNILLFQNIDGKELCKMTKDDFQRLT PSYNADILLSHLHYLRETPLPHLTSDDVDKALQNSPRLMHARNTGGAAFIFPNTSVYPEATQRITTRPDLPYEPPRRSAWTGHGHPTPQS KAAQPSPSTVPKTEDQRPQLDPYQILGPTSSRLANPGSGQIQLWQFLLELLSDSSNSSCITWEGTNGEFKMTDPDEVARRWGERKSKPNM NYDKLSRALRYYYDKNIMTKVHGKRYAYKFDFHGIAQALQPHPPESSLYKYPSDLPYMGSYHAHPQKMNFVAPHPPALPVTSSSFFAAPN
P11308-1	MIQTVPDPAAHIKEALSVVSEDQSLFECAYGTPHLAKTEMTASSSSDYGQTSKMSPRVPQQDWLSQPPARVTIKMECNPSQVNGSRNSPD ECSVAKGGKMVGSPDTVGMNYGSYMEEKHMPPPNMTTNERRVIVPADPTLWSTDHVRQWLEWAVKEYGLPDVNILLFQNIDGKELCKMTK DDFQRLTPSYNADILLSHLHYLRETPLPHLTSDDVDKALQNSPRLMHARNTDLPYEPPRRSAWTGHGHPTPQSKAAQPSPSTVPKTEDQR PQLDPYQILGPTSSRLANPGSGQIQLWQFLLELLSDSSNSSCITWEGTNGEFKMTDPDEVARRWGERKSKPNMNYDKLSRALRYYYDKNI MTKVHGKRYAYKFDFHGIAQALQPHPPESSLYKYPSDLPYMGSYHAHPQKMNFVAPHPPALPVTSSSFFAAPNPYWNSPTGGIYPNTRLP
P11308-2	MVGSPDTVGMNYGSYMEEKHMPPPNMTTNERRVIVPADPTLWSTDHVRQWLEWAVKEYGLPDVNILLFQNIDGKELCKMTKDDFQRLTPS YNADILLSHLHYLRETPLPHLTSDDVDKALQNSPRLMHARNTDLPYEPPRRSAWTGHGHPTPQSKAAQPSPSTVPKTEDQRPQLDPYQIL GPTSSRLANPGSGQIQLWQFLLELLSDSSNSSCITWEGTNGEFKMTDPDEVARRWGERKSKPNMNYDKLSRALRYYYDKNIMTKVHGKRY AYKFDFHGIAQALQPHPPESSLYKYPSDLPYMGSYHAHPQKMNFVAPHPPALPVTSSSFFAAPNPYWNSPTGGIYPNTRLPTSHMPSHLG
P11308-3	MIQTVPDPAAHIKEALSVVSEDQSLFECAYGTPHLAKTEMTASSSSDYGQTSKMSPRVPQQDWLSQPPARVTIKMECNPSQVNGSRNSPD ECSVAKGGKMVGSPDTVGMNYGSYMEEKHMPPPNMTTNERRVIVPADPTLWSTDHVRQWLEWAVKEYGLPDVNILLFQNIDGKELCKMTK DDFQRLTPSYNADILLSHLHYLRETPLPHLTSDDVDKALQNSPRLMHARNTGGAAFIFPNTSVYPEATQRITTRPDLPYEPPRRSAWTGH GHPTPQSKAAQPSPSTVPKTEDQRPQLDPYQILGPTSSRLANPGSGQIQLWQFLLELLSDSSNSSCITWEGTNGEFKMTDPDEVARRWGE RKSKPNMNYDKLSRALRYYYDKNIMTKVHGKRYAYKFDFHGIAQALQPHPPESSLYKYPSDLPYMGSYHAHPQKMNFVAPHPPALPVTSS
P11308-5	MIQTVPDPAAHIKEALSVVSEDQSLFECAYGTPHLAKTEMTASSSSDYGQTSKMSPRVPQQDWLSQPPARVTIKMECNPSQVNGSRNSPD ECSVAKGGKMVGSPDTVGMNYGSYMEEKHMPPPNMTTNERRVIVPADPTLWSTDHVRQWLEWAVKEYGLPDVNILLFQNIDGKELCKMTK DDFQRLTPSYNADILLSHLHYLRETPLPHLTSDDVDKALQNSPRLMHARNTGGAAFIFPNTSVYPEATQRITTRPDLPYEPPRRSAWTGH
P11308-6	MIQTVPDPAAHIKEALSVVSEDQSLFECAYGTPHLAKTEMTASSSSDYGQTSKMSPRVPQQDWLSQPPARVTIKMECNPSQVNGSRNSPD ECSVAKGGKMVGSPDTVGMNYGSYMEEKHMPPPNMTTNERRVIVPADPTLWSTDHVRQWLEWAVKEYGLPDVNILLFQNIDGKELCKMTK DDFQRLTPSYNADILLSHLHYLRETPLPHLTSDDVDKALQNSPRLMHARNTGGAAFIFPNTSVYPEATQRITTRPGTKTPLCDLFIERHP

Protein Functional Features

Main function of this protein. (from UniProt)

ERG (go to UniProt):P11308

Retention analysis result of protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at
download page
* Minus value of BPloci means that the break pointn is located before the CDS.

- Retained protein feature among the 13 regional features.

Accession_id	Subsection	Start	End	Funcitonal feature	Splicing information
P11308	DNA binding	311	391	Note=ETS;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00237	Type=Deletion;Start=311;End=479
P11308	DNA binding	311	391	Note=ETS;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00237	Type=Substitution;Start=249;End=318
P11308	DNA binding	311	391	Note=ETS;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00237	Type=Deletion;Start=319;End=479
P11308	Region	34	56	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=1;End=92
P11308	Region	72	92	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=1;End=92
P11308	Region	242	293	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=225;End=248
P11308	Region	242	293	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=225;End=248
P11308	Region	242	293	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Substitution;Start=249;End=318
P11308	Compositional bias	263	285	Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Substitution;Start=249;End=318

Gene Isoform Structures and Expression Levels for ERG

Gene structures of our canonical and alternative spliced genes of ERG
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Expression levels of gene isoforms across GTEx.

Expression levels of gene isoforms across TCGA.

Protein Structures

PDB and CIF files of the predicted protein structures
* Here we show the 3D structure of the proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format.

3D view using mol* of P11308-4

3D view using mol* of P11308-1

3D view using mol* of P11308-2

3D view using mol* of P11308-3

3D view using mol* of P11308-5

3D view using mol* of P11308-6

pLDDT Score Distribution

pLDDT score distribution of the predicted protein structures from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.

pLDDT distribution across the protein length of P11308-4

pLDDT distribution across the protein length of P11308-1

pLDDT distribution across the protein length of P11308-2

pLDDT distribution across the protein length of P11308-3

pLDDT distribution across the protein length of P11308-5

pLDDT distribution across the protein length of P11308-6

Ramachandran Plot of Protein Structures

Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this protein peptide.

Ramachandran plot of P11308-4

Ramachandran plot of P11308-3

Potential Active Site Information

The potential binding sites of these proteins were identified using SiteMap, a module of the Schrodinger suite.

UniProt-id	Site score	Size	D score	Volume	Exposure	Enclosure	Contact	Phobic	Philic	Balance	Don/Acc	Residues
P11308-4	1.1	156	1.193	534.394	0.567	0.691	0.921	1.723	0.496	3.478	1.231	150,151,173,183,186,187,189,190,191,193,194,208,21 1,212,215,218,220,221,222,224,225,226,227,228,229, 230,231
P11308-1	0.938	81	0.993	245.245	0.671	0.606	0.783	0.847	0.665	1.273	1.255	135,136,137,138,140,201,202,203,205,206,207,208,20 9,210,278,281,282,284,285
P11308-2	1.051	103	1.097	509.012	0.701	0.714	0.782	0.662	0.832	0.796	0.908	28,30,31,32,33,35,36,37,42,48,49,50,52,53,56,57,99 ,102,103,106,108,183,186,187,276,279,280,283
P11308-3	0.707	48	0.681	141.316	0.741	0.576	0.764	0.232	0.968	0.24	1.121	310,311,312,315,317,318,319,321,322,382,384,404,40 5,406,407,408,409
P11308-5	0.888	79	0.823	229.467	0.559	0.652	0.934	0.261	1.237	0.211	0.371	128,129,130,131,219,222,224,225,227,228,231,233,23 4,235,236,237,238,239
P11308-6	1.021	124	1.075	287.434	0.575	0.66	0.914	1.027	0.799	1.285	0.808	222,223,224,225,227,228,231,234,235,236,237,238,26 3,266,274,277,278,280,281,282

Protein Structure and Feature Comparision

Protein Structure Comparision Using Template Modeling Scores (TM-score).

Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Canonical validated structure (PDB)(green)

3D view using mol* of P11308-4_P11308-4_4irh_A.pdb

Protein Structure Comparision Visualization with mol*. between Canonical validated structure (PDB)(orange) vs Alternative predicted structure (AF2)(green)

3D view using mol* of P11308-4_4irh_A_P11308-1.pdb

3D view using mol* of P11308-4_4irh_A_P11308-2.pdb

3D view using mol* of P11308-4_4irh_A_P11308-3.pdb

3D view using mol* of P11308-4_4irh_A_P11308-5.pdb

3D view using mol* of P11308-4_4irh_A_P11308-6.pdb

Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Alternative predicted structure (AF2)(green)

3D view using mol* of P11308-4_P11308-1.pdb

3D view using mol* of P11308-4_P11308-2.pdb

3D view using mol* of P11308-4_P11308-3.pdb

3D view using mol* of P11308-4_P11308-5.pdb

3D view using mol* of P11308-4_P11308-6.pdb

Protein Feature Comparison of the protein sequendary structures among the protiens.

./stats/secondary_structure/figure/P11308-4_vs_P11308-1.png