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:PPARGC1B

Protein Summary

Gene summary

Gene name: PPARGC1B
ASpdb.0 ID: 133522
	Gene
Gene symbol	PPARGC1B
Gene ID	133522
Gene name	PPARG coactivator 1 beta
Synonyms	ERRL1\|PERC\|PGC-1(beta)\|PGC1B
Cytomap	5q32
Type of gene	protein-coding
Description	peroxisome proliferator-activated receptor gamma coactivator 1-betaPGC-1-related estrogen receptor alpha coactivatorPPAR-gamma coactivator 1-betaPPARAGCIbetaPPARGC-1-betaPPARgamma coactivator 1 betaperoxisome proliferator-activated receptor gamma, c
Modification date	20240403
UniProtAcc	Q86YN6

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

Partner	Gene	GO ID	GO term	PubMed ID
Gene	PPARGC1B	GO:0003712	transcription coregulator activity	11854298
Gene	PPARGC1B	GO:0005634	nucleus	11854298
Gene	PPARGC1B	GO:0005654	nucleoplasm	-
Gene	PPARGC1B	GO:0005829	cytosol	-
Gene	PPARGC1B	GO:0006355	regulation of DNA-templated transcription	23836911
Gene	PPARGC1B	GO:0016592	mediator complex	11854298
Gene	PPARGC1B	GO:0030331	nuclear estrogen receptor binding	11854298
Gene	PPARGC1B	GO:0030374	nuclear receptor coactivator activity	11854298
Gene	PPARGC1B	GO:0030520	intracellular estrogen receptor signaling pathway	11854298
Gene	PPARGC1B	GO:0045944	positive regulation of transcription by RNA polymerase II	11854298

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
Q86YN6-1	Q86YN6-1_6d0y_B.pdb	6D0Y	X-ray	2.68	B	1004	1022

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

Q86YN6

PPARGC1B

Q86YN6-1

Q86YN6-2

1023

1002

Substitution

MAGNDCGALLDEELSSFFLNYLADTQ

MGVYK

Q86YN6

PPARGC1B

Q86YN6-1

Q86YN6-4

1023

996

Substitution

MAGNDCGALLDEELSSFFLNYLADTQ

MGVYK

Q86YN6

PPARGC1B

Q86YN6-1

Q86YN6-4

1023

996

991

1023

Substitution

DSNSEEALPASGKSKYEAMDFDSLLKEAQQSLH

GKPLKPSHSLVRLKAWEAVPSLNKTQS

970

996

Q86YN6

PPARGC1B

Q86YN6-1

Q86YN6-5

1023

984

156

194

Deletion

none

155

Q86YN6

PPARGC1B

Q86YN6-1

Q86YN6-6

1023

959

Substitution

MAGNDCGALLDEELSSFFLNYLADTQ

Q86YN6

PPARGC1B

Q86YN6-1

Q86YN6-6

1023

959

156

194

Deletion

none

130

Multiple sequence alignment of our canonical and alternatively spliced PPARGC1B

Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of PPARGC1B

UniProt-id	ENSG	ENST	ENSP
Q86YN6-1	ENSG00000155846.17	ENST00000309241.10	ENSP00000312649.5
Q86YN6-5	ENSG00000155846.17	ENST00000360453.8	ENSP00000353638.4
Q86YN6-6	ENSG00000155846.17	ENST00000403750.5	ENSP00000384403.1

UniProt-id	NM ID	NP ID
Q86YN6-1	NM_133263.3	NP_573570.3
Q86YN6-2	XM_005268372.4	XP_005268429.1
Q86YN6-5	NM_001172698.1	NP_001166169.1
Q86YN6-6	NM_001172699.1	NP_001166170.1

Amino acid sequences of our canonical and alternatively spliced PPARGC1B

accession_id	Protein sequence
Q86YN6-1	MAGNDCGALLDEELSSFFLNYLADTQGGGSGEEQLYADFPELDLSQLDASDFDSATCFGELQWCPENSETEPNQYSPDDSELFQIDSENE ALLAELTKTLDDIPEDDVGLAAFPALDGGDALSCTSASPAPSSAPPSPAPEKPSAPAPEVDELSLLQKLLLATSYPTSSSDTQKEGTAWR QAGLRSKSQRPCVKADSTQDKKAPMMQSQSRSCTELHKHLTSAQCCLQDRGLQPPCLQSPRLPAKEDKEPGEDCPSPQPAPASPRDSLAL GRADPGAPVSQEDMQAMVQLIRYMHTYCLPQRKLPPQTPEPLPKACSNPSQQVRSRPWSRHHSKASWAEFSILRELLAQDVLCDVSKPYR LATPVYASLTPRSRPRPPKDSQASPGRPSSVEEVRIAASPKSTGPRPSLRPLRLEVKREVRRPARLQQQEEEDEEEEEEEEEEEKEEEEE WGRKRPGRGLPWTKLGRKLESSVCPVRRSRRLNPELGPWLTFADEPLVPSEPQGALPSLCLAPKAYDVERELGSPTDEDSGQDQQLLRGP QIPALESPCESGCGDMDEDPSCPQLPPRDSPRCLMLALSQSDPTFGKKSFEQTLTVELCGTAGLTPPTTPPYKPTEEDPFKPDIKHSLGK EIALSLPSPEGLSLKATPGAAHKLPKKHPERSELLSHLRHATAQPASQAGQKRPFSCSFGDHDYCQVLRPEGVLQRKVLRSWEPSGVHLE DWPQQGAPWAEAQAPGREEDRSCDAGAPPKDSTLLRDHEIRASLTKHFGLLETALEEEDLASCKSPEYDTVFEDSSSSSGESSFLPEEEE EEGEEEEEDDEEEDSGVSPTCSDHCPYQSPPSKANRQLCSRSRSSSGSSPCHSWSPATRRNFRCESRGPCSDRTPSIRHARKRREKAIGE GRVVYIQNLSSDMSSRELKRRFEVFGEIEECEVLTRNRRGEKYGFITYRCSEHAALSLTKGAALRKRNEPSFQLSYGGLRHFCWPRYTDY
Q86YN6-2	MGVYKGGGSGEEQLYADFPELDLSQLDASDFDSATCFGELQWCPENSETEPNQYSPDDSELFQIDSENEALLAELTKTLDDIPEDDVGLA AFPALDGGDALSCTSASPAPSSAPPSPAPEKPSAPAPEVDELSLLQKLLLATSYPTSSSDTQKEGTAWRQAGLRSKSQRPCVKADSTQDK KAPMMQSQSRSCTELHKHLTSAQCCLQDRGLQPPCLQSPRLPAKEDKEPGEDCPSPQPAPASPRDSLALGRADPGAPVSQEDMQAMVQLI RYMHTYCLPQRKLPPQTPEPLPKACSNPSQQVRSRPWSRHHSKASWAEFSILRELLAQDVLCDVSKPYRLATPVYASLTPRSRPRPPKDS QASPGRPSSVEEVRIAASPKSTGPRPSLRPLRLEVKREVRRPARLQQQEEEDEEEEEEEEEEEKEEEEEWGRKRPGRGLPWTKLGRKLES SVCPVRRSRRLNPELGPWLTFADEPLVPSEPQGALPSLCLAPKAYDVERELGSPTDEDSGQDQQLLRGPQIPALESPCESGCGDMDEDPS CPQLPPRDSPRCLMLALSQSDPTFGKKSFEQTLTVELCGTAGLTPPTTPPYKPTEEDPFKPDIKHSLGKEIALSLPSPEGLSLKATPGAA HKLPKKHPERSELLSHLRHATAQPASQAGQKRPFSCSFGDHDYCQVLRPEGVLQRKVLRSWEPSGVHLEDWPQQGAPWAEAQAPGREEDR SCDAGAPPKDSTLLRDHEIRASLTKHFGLLETALEEEDLASCKSPEYDTVFEDSSSSSGESSFLPEEEEEEGEEEEEDDEEEDSGVSPTC SDHCPYQSPPSKANRQLCSRSRSSSGSSPCHSWSPATRRNFRCESRGPCSDRTPSIRHARKRREKAIGEGRVVYIQNLSSDMSSRELKRR FEVFGEIEECEVLTRNRRGEKYGFITYRCSEHAALSLTKGAALRKRNEPSFQLSYGGLRHFCWPRYTDYDSNSEEALPASGKSKYEAMDF
Q86YN6-4	MGVYKGGGSGEEQLYADFPELDLSQLDASDFDSATCFGELQWCPENSETEPNQYSPDDSELFQIDSENEALLAELTKTLDDIPEDDVGLA AFPALDGGDALSCTSASPAPSSAPPSPAPEKPSAPAPEVDELSLLQKLLLATSYPTSSSDTQKEGTAWRQAGLRSKSQRPCVKADSTQDK KAPMMQSQSRSCTELHKHLTSAQCCLQDRGLQPPCLQSPRLPAKEDKEPGEDCPSPQPAPASPRDSLALGRADPGAPVSQEDMQAMVQLI RYMHTYCLPQRKLPPQTPEPLPKACSNPSQQVRSRPWSRHHSKASWAEFSILRELLAQDVLCDVSKPYRLATPVYASLTPRSRPRPPKDS QASPGRPSSVEEVRIAASPKSTGPRPSLRPLRLEVKREVRRPARLQQQEEEDEEEEEEEEEEEKEEEEEWGRKRPGRGLPWTKLGRKLES SVCPVRRSRRLNPELGPWLTFADEPLVPSEPQGALPSLCLAPKAYDVERELGSPTDEDSGQDQQLLRGPQIPALESPCESGCGDMDEDPS CPQLPPRDSPRCLMLALSQSDPTFGKKSFEQTLTVELCGTAGLTPPTTPPYKPTEEDPFKPDIKHSLGKEIALSLPSPEGLSLKATPGAA HKLPKKHPERSELLSHLRHATAQPASQAGQKRPFSCSFGDHDYCQVLRPEGVLQRKVLRSWEPSGVHLEDWPQQGAPWAEAQAPGREEDR SCDAGAPPKDSTLLRDHEIRASLTKHFGLLETALEEEDLASCKSPEYDTVFEDSSSSSGESSFLPEEEEEEGEEEEEDDEEEDSGVSPTC SDHCPYQSPPSKANRQLCSRSRSSSGSSPCHSWSPATRRNFRCESRGPCSDRTPSIRHARKRREKAIGEGRVVYIQNLSSDMSSRELKRR FEVFGEIEECEVLTRNRRGEKYGFITYRCSEHAALSLTKGAALRKRNEPSFQLSYGGLRHFCWPRYTDYGKPLKPSHSLVRLKAWEAVPS
Q86YN6-5	MAGNDCGALLDEELSSFFLNYLADTQGGGSGEEQLYADFPELDLSQLDASDFDSATCFGELQWCPENSETEPNQYSPDDSELFQIDSENE ALLAELTKTLDDIPEDDVGLAAFPALDGGDALSCTSASPAPSSAPPSPAPEKPSAPAPEVDELSLADSTQDKKAPMMQSQSRSCTELHKH LTSAQCCLQDRGLQPPCLQSPRLPAKEDKEPGEDCPSPQPAPASPRDSLALGRADPGAPVSQEDMQAMVQLIRYMHTYCLPQRKLPPQTP EPLPKACSNPSQQVRSRPWSRHHSKASWAEFSILRELLAQDVLCDVSKPYRLATPVYASLTPRSRPRPPKDSQASPGRPSSVEEVRIAAS PKSTGPRPSLRPLRLEVKREVRRPARLQQQEEEDEEEEEEEEEEEKEEEEEWGRKRPGRGLPWTKLGRKLESSVCPVRRSRRLNPELGPW LTFADEPLVPSEPQGALPSLCLAPKAYDVERELGSPTDEDSGQDQQLLRGPQIPALESPCESGCGDMDEDPSCPQLPPRDSPRCLMLALS QSDPTFGKKSFEQTLTVELCGTAGLTPPTTPPYKPTEEDPFKPDIKHSLGKEIALSLPSPEGLSLKATPGAAHKLPKKHPERSELLSHLR HATAQPASQAGQKRPFSCSFGDHDYCQVLRPEGVLQRKVLRSWEPSGVHLEDWPQQGAPWAEAQAPGREEDRSCDAGAPPKDSTLLRDHE IRASLTKHFGLLETALEEEDLASCKSPEYDTVFEDSSSSSGESSFLPEEEEEEGEEEEEDDEEEDSGVSPTCSDHCPYQSPPSKANRQLC SRSRSSSGSSPCHSWSPATRRNFRCESRGPCSDRTPSIRHARKRREKAIGEGRVVYIQNLSSDMSSRELKRRFEVFGEIEECEVLTRNRR
Q86YN6-6	MGGGSGEEQLYADFPELDLSQLDASDFDSATCFGELQWCPENSETEPNQYSPDDSELFQIDSENEALLAELTKTLDDIPEDDVGLAAFPA LDGGDALSCTSASPAPSSAPPSPAPEKPSAPAPEVDELSLADSTQDKKAPMMQSQSRSCTELHKHLTSAQCCLQDRGLQPPCLQSPRLPA KEDKEPGEDCPSPQPAPASPRDSLALGRADPGAPVSQEDMQAMVQLIRYMHTYCLPQRKLPPQTPEPLPKACSNPSQQVRSRPWSRHHSK ASWAEFSILRELLAQDVLCDVSKPYRLATPVYASLTPRSRPRPPKDSQASPGRPSSVEEVRIAASPKSTGPRPSLRPLRLEVKREVRRPA RLQQQEEEDEEEEEEEEEEEKEEEEEWGRKRPGRGLPWTKLGRKLESSVCPVRRSRRLNPELGPWLTFADEPLVPSEPQGALPSLCLAPK AYDVERELGSPTDEDSGQDQQLLRGPQIPALESPCESGCGDMDEDPSCPQLPPRDSPRCLMLALSQSDPTFGKKSFEQTLTVELCGTAGL TPPTTPPYKPTEEDPFKPDIKHSLGKEIALSLPSPEGLSLKATPGAAHKLPKKHPERSELLSHLRHATAQPASQAGQKRPFSCSFGDHDY CQVLRPEGVLQRKVLRSWEPSGVHLEDWPQQGAPWAEAQAPGREEDRSCDAGAPPKDSTLLRDHEIRASLTKHFGLLETALEEEDLASCK SPEYDTVFEDSSSSSGESSFLPEEEEEEGEEEEEDDEEEDSGVSPTCSDHCPYQSPPSKANRQLCSRSRSSSGSSPCHSWSPATRRNFRC ESRGPCSDRTPSIRHARKRREKAIGEGRVVYIQNLSSDMSSRELKRRFEVFGEIEECEVLTRNRRGEKYGFITYRCSEHAALSLTKGAAL

Protein Functional Features

Main function of this protein. (from UniProt)

PPARGC1B (go to UniProt):Q86YN6

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
Q86YN6	Region	1	91	Note=Abolishes DNA transcriptional activity when missing	Type=Substitution;Start=1;End=26
Q86YN6	Region	1	91	Note=Abolishes DNA transcriptional activity when missing	Type=Substitution;Start=1;End=26
Q86YN6	Region	1	91	Note=Abolishes DNA transcriptional activity when missing	Type=Substitution;Start=1;End=26
Q86YN6	Region	165	210	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=156;End=194
Q86YN6	Region	165	210	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=156;End=194
Q86YN6	Motif	156	160	Note=LXXLL motif 1	Type=Deletion;Start=156;End=194
Q86YN6	Motif	156	160	Note=LXXLL motif 1	Type=Deletion;Start=156;End=194
Q86YN6	Compositional bias	165	184	Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=156;End=194
Q86YN6	Compositional bias	165	184	Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=156;End=194

Gene Isoform Structures and Expression Levels for PPARGC1B

Gene structures of our canonical and alternative spliced genes of PPARGC1B
* 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 Q86YN6-1

3D view using mol* of Q86YN6-2

3D view using mol* of Q86YN6-4

3D view using mol* of Q86YN6-5

3D view using mol* of Q86YN6-6

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 Q86YN6-1

pLDDT distribution across the protein length of Q86YN6-2

pLDDT distribution across the protein length of Q86YN6-4

pLDDT distribution across the protein length of Q86YN6-5

pLDDT distribution across the protein length of Q86YN6-6

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 Q86YN6-1

Ramachandran plot of Q86YN6-2

Ramachandran plot of Q86YN6-5

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
Q86YN6-1	0.919	76	0.915	243.53	0.62	0.709	0.972	0.741	1.013	0.731	0.855	891,894,895,898,903,905,945,976,977,979,980,981,98 2,983,984,985,986,987,988,989
Q86YN6-2	0.995	183	1.035	622.202	0.672	0.654	0.811	0.547	0.914	0.599	0.843	416,417,419,420,422,423,424,425,426,427,429,430,86 6,867,869,870,871,873,874,877,924,958,959,961,962, 963,964,965,966,968,969,971
Q86YN6-4	1.01	147	1.05	454.132	0.641	0.672	0.798	0.866	0.9	0.963	1.015	415,416,418,419,420,422,423,425,426,429,866,867,87 0,871,873,874,877,957,958,961,962,964,965,966
Q86YN6-5	0.887	70	0.929	166.698	0.622	0.601	0.857	1.2	0.669	1.794	0.431	172,173,174,176,177,180,181,247,250,251,253,254,25 8
Q86YN6-6	1.006	178	1.062	769.349	0.732	0.638	0.768	0.596	0.801	0.745	0.764	371,372,373,375,376,379,380,383,819,820,821,823,82 6,827,829,830,831,834,841,843,844,845,850,851,852, 855,865,866,867,868,869,870,872,876,877,878,879,88 1,906,915,916,917,918,919,920,921,922,924,926

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 Q86YN6-1_Q86YN6-1_6d0y_B.pdb

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

3D view using mol* of Q86YN6-1_6d0y_B_Q86YN6-2.pdb

3D view using mol* of Q86YN6-1_6d0y_B_Q86YN6-4.pdb

3D view using mol* of Q86YN6-1_6d0y_B_Q86YN6-5.pdb

3D view using mol* of Q86YN6-1_6d0y_B_Q86YN6-6.pdb

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

3D view using mol* of Q86YN6-1_Q86YN6-2.pdb

3D view using mol* of Q86YN6-1_Q86YN6-4.pdb

3D view using mol* of Q86YN6-1_Q86YN6-5.pdb

3D view using mol* of Q86YN6-1_Q86YN6-6.pdb

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

./stats/secondary_structure/figure/Q86YN6-1_vs_Q86YN6-2.png

./stats/secondary_structure/figure/Q86YN6-1_vs_Q86YN6-4.png

./stats/secondary_structure/figure/Q86YN6-1_vs_Q86YN6-5.png

./stats/secondary_structure/figure/Q86YN6-1_vs_Q86YN6-6.png

Protein Feature Comparison of the relative accessible surface area (ASA) among the protiens.

./stats/relative_asa/Q86YN6-1_vs_Q86YN6-2.png

./stats/relative_asa/Q86YN6-1_vs_Q86YN6-4.png

./stats/relative_asa/Q86YN6-1_vs_Q86YN6-5.png

./stats/relative_asa/Q86YN6-1_vs_Q86YN6-6.png

Protein-Protein Interaction

Interactors from UniProt.

Accession_id

Subsection

Start

End

Funcitonal feature

Splicing information

Interactors from STRING.

Gene name

Interactors

Related Drugs to PPARGC1B

Drugs targeting this gene/protein.
(DrugBank)

UniProt accession	Gene name	DrugBank ID	Drug name	Drug group	Actions
Q86YN6	PPARGC1B	DB01118	Amiodarone	approved, investigational	agonist

Related Diseases to PPARGC1B

Previous studies relating to the alternative splicing of PPARGC1B and disease information from the MeSH term (PubMed)

Gene

PMID

Title

Abstract

MeSH ID

MeSH term

Clinically important variants in PPARGC1B

(ClinVar, 04/20/2024)

accession_id

uniprot_id

gene_name

Type

Variant

Clinical_significance