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:CAPN3

Protein Summary

Gene summary

Gene name: CAPN3
ASpdb.0 ID: 825
	Gene
Gene symbol	CAPN3
Gene ID	825
Gene name	calpain 3
Synonyms	CANP3\|CANPL3\|LGMD2\|LGMD2A\|LGMDD4\|LGMDR1\|nCL-1\|p94
Cytomap	15q15.1
Type of gene	protein-coding
Description	calpain-3calpain p94, large [catalytic] subunitcalpain, large polypeptide L3muscle-specific calcium-activated neutral protease 3 large subunitnew calpain 1
Modification date	20240407
UniProtAcc	P20807

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

Partner	Gene	GO ID	GO term	PubMed ID
Gene	CAPN3	GO:0003824	catalytic activity	9642272
Gene	CAPN3	GO:0005634	nucleus	19386580
Gene	CAPN3	GO:0005730	nucleolus	27657329
Gene	CAPN3	GO:0005737	cytoplasm	19386580\|19556129
Gene	CAPN3	GO:0006508	proteolysis	9642272\|18310072\|19386580\|20694146
Gene	CAPN3	GO:0008233	peptidase activity	9642272\|23707407
Gene	CAPN3	GO:0030163	protein catabolic process	27657329
Gene	CAPN3	GO:0033234	negative regulation of protein sumoylation	20694146
Gene	CAPN3	GO:0050790	regulation of catalytic activity	20694146
Gene	CAPN3	GO:0055103	ligase regulator activity	20694146
Gene	CAPN3	GO:0097264	self proteolysis	9642272
Gene	CAPN3	GO:1990092	calcium-dependent self proteolysis	12482600

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
P20807-1	P20807-1_6bjd_A.pdb	6BJD	X-ray	2.8	A	53	417

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

P20807

CAPN3

P20807-1

P20807-2

821

729

268

315

Deletion

none

267

P20807

CAPN3

P20807-1

P20807-2

821

729

595

638

Deletion

none

546

P20807

CAPN3

P20807-1

P20807-3

821

815

595

600

Deletion

none

594

P20807

CAPN3

P20807-1

P20807-4

821

309

512

Deletion

none

P20807

CAPN3

P20807-1

P20807-5

821

156

665

Deletion

none

Multiple sequence alignment of our canonical and alternatively spliced CAPN3

Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of CAPN3

UniProt-id	ENSG	ENST	ENSP
P20807-1	ENSG00000092529.26	ENST00000397163.8	ENSP00000380349.3
P20807-2	ENSG00000092529.26	ENST00000349748.8	ENSP00000183936.4
P20807-3	ENSG00000092529.26	ENST00000357568.8	ENSP00000350181.3
P20807-4	ENSG00000092529.26	ENST00000397200.8	ENSP00000380384.4
P20807-5	ENSG00000092529.26	ENST00000337571.9	ENSP00000336840.4
P20807-5	ENSG00000092529.26	ENST00000397204.9	ENSP00000380387.4
P20807-5	ENSG00000092529.26	ENST00000569136.6	ENSP00000455254.1
P20807-5	ENSG00000092529.26	ENST00000673692.1	ENSP00000501138.1
P20807-5	ENSG00000092529.26	ENST00000673771.1	ENSP00000501023.1
P20807-5	ENSG00000092529.26	ENST00000673851.1	ENSP00000501142.1
P20807-5	ENSG00000092529.26	ENST00000673886.1	ENSP00000501155.1
P20807-5	ENSG00000092529.26	ENST00000673890.1	ENSP00000501293.1
P20807-5	ENSG00000092529.26	ENST00000673928.1	ENSP00000501099.1
P20807-5	ENSG00000092529.26	ENST00000673936.1	ENSP00000501189.1
P20807-5	ENSG00000092529.26	ENST00000674018.1	ENSP00000501271.1
P20807-5	ENSG00000092529.26	ENST00000674093.1	ENSP00000501303.1
P20807-5	ENSG00000092529.26	ENST00000674119.1	ENSP00000501217.1
P20807-5	ENSG00000092529.26	ENST00000674139.1	ENSP00000501054.1
P20807-5	ENSG00000092529.26	ENST00000674146.1	ENSP00000501175.1
P20807-5	ENSG00000092529.26	ENST00000674149.1	ENSP00000501112.1

UniProt-id	NM ID	NP ID
P20807-1	NM_000070.2	NP_000061.1
P20807-2	NM_173087.1	NP_775110.1
P20807-3	NM_024344.1	NP_077320.1
P20807-4	NM_173088.1	NP_775111.1
P20807-5	NM_173089.1	NP_775112.1
P20807-5	NM_173090.1	NP_775113.1

Amino acid sequences of our canonical and alternatively spliced CAPN3

accession_id	Protein sequence
P20807-1	MPTVISASVAPRTAAEPRSPGPVPHPAQSKATEAGGGNPSGIYSAIISRNFPIIGVKEKTFEQLHKKCLEKKVLYVDPEFPPDETSLFYS QKFPIQFVWKRPPEICENPRFIIDGANRTDICQGELGDCWFLAAIACLTLNQHLLFRVIPHDQSFIENYAGIFHFQFWRYGEWVDVVIDD CLPTYNNQLVFTKSNHRNEFWSALLEKAYAKLHGSYEALKGGNTTEAMEDFTGGVAEFFEIRDAPSDMYKIMKKAIERGSLMGCSIDDGT NMTYGTSPSGLNMGELIARMVRNMDNSLLQDSDLDPRGSDERPTRTIIPVQYETRMACGLVRGHAYSVTGLDEVPFKGEKVKLVRLRNPW GQVEWNGSWSDRWKDWSFVDKDEKARLQHQVTEDGEFWMSYEDFIYHFTKLEICNLTADALQSDKLQTWTVSVNEGRWVRGCSAGGCRNF PDTFWTNPQYRLKLLEEDDDPDDSEVICSFLVALMQKNRRKDRKLGASLFTIGFAIYEVPKEMHGNKQHLQKDFFLYNASKARSKTYINM REVSQRFRLPPSEYVIVPSTYEPHQEGEFILRVFSEKRNLSEEVENTISVDRPVKKKKTKPIIFVSDRANSNKELGVDQESEEGKGKTSP DKQKQSPQPQPGSSDQESEEQQQFRNIFKQIAGDDMEICADELKKVLNTVVNKHKDLKTHGFTLESCRSMIALMDTDGSGKLNLQEFHHL WNKIKAWQKIFKHYDTDQSGTINSYEMRNAVNDAGFHLNNQLYDIITMRYADKHMNIDFDSFICCFVRLEGMFRAFHAFDKDGDGIIKLN
P20807-2	MPTVISASVAPRTAAEPRSPGPVPHPAQSKATEAGGGNPSGIYSAIISRNFPIIGVKEKTFEQLHKKCLEKKVLYVDPEFPPDETSLFYS QKFPIQFVWKRPPEICENPRFIIDGANRTDICQGELGDCWFLAAIACLTLNQHLLFRVIPHDQSFIENYAGIFHFQFWRYGEWVDVVIDD CLPTYNNQLVFTKSNHRNEFWSALLEKAYAKLHGSYEALKGGNTTEAMEDFTGGVAEFFEIRDAPSDMYKIMKKAIERGSLMGCSIDTII PVQYETRMACGLVRGHAYSVTGLDEVPFKGEKVKLVRLRNPWGQVEWNGSWSDRWKDWSFVDKDEKARLQHQVTEDGEFWMSYEDFIYHF TKLEICNLTADALQSDKLQTWTVSVNEGRWVRGCSAGGCRNFPDTFWTNPQYRLKLLEEDDDPDDSEVICSFLVALMQKNRRKDRKLGAS LFTIGFAIYEVPKEMHGNKQHLQKDFFLYNASKARSKTYINMREVSQRFRLPPSEYVIVPSTYEPHQEGEFILRVFSEKRNLSEEVENTI SVDRPVPQPGSSDQESEEQQQFRNIFKQIAGDDMEICADELKKVLNTVVNKHKDLKTHGFTLESCRSMIALMDTDGSGKLNLQEFHHLWN KIKAWQKIFKHYDTDQSGTINSYEMRNAVNDAGFHLNNQLYDIITMRYADKHMNIDFDSFICCFVRLEGMFRAFHAFDKDGDGIIKLNVL
P20807-3	MPTVISASVAPRTAAEPRSPGPVPHPAQSKATEAGGGNPSGIYSAIISRNFPIIGVKEKTFEQLHKKCLEKKVLYVDPEFPPDETSLFYS QKFPIQFVWKRPPEICENPRFIIDGANRTDICQGELGDCWFLAAIACLTLNQHLLFRVIPHDQSFIENYAGIFHFQFWRYGEWVDVVIDD CLPTYNNQLVFTKSNHRNEFWSALLEKAYAKLHGSYEALKGGNTTEAMEDFTGGVAEFFEIRDAPSDMYKIMKKAIERGSLMGCSIDDGT NMTYGTSPSGLNMGELIARMVRNMDNSLLQDSDLDPRGSDERPTRTIIPVQYETRMACGLVRGHAYSVTGLDEVPFKGEKVKLVRLRNPW GQVEWNGSWSDRWKDWSFVDKDEKARLQHQVTEDGEFWMSYEDFIYHFTKLEICNLTADALQSDKLQTWTVSVNEGRWVRGCSAGGCRNF PDTFWTNPQYRLKLLEEDDDPDDSEVICSFLVALMQKNRRKDRKLGASLFTIGFAIYEVPKEMHGNKQHLQKDFFLYNASKARSKTYINM REVSQRFRLPPSEYVIVPSTYEPHQEGEFILRVFSEKRNLSEEVENTISVDRPVPIIFVSDRANSNKELGVDQESEEGKGKTSPDKQKQS PQPQPGSSDQESEEQQQFRNIFKQIAGDDMEICADELKKVLNTVVNKHKDLKTHGFTLESCRSMIALMDTDGSGKLNLQEFHHLWNKIKA WQKIFKHYDTDQSGTINSYEMRNAVNDAGFHLNNQLYDIITMRYADKHMNIDFDSFICCFVRLEGMFRAFHAFDKDGDGIIKLNVLEWLQ
P20807-4	MHGNKQHLQKDFFLYNASKARSKTYINMREVSQRFRLPPSEYVIVPSTYEPHQEGEFILRVFSEKRNLSEEVENTISVDRPVKKKKTKPI IFVSDRANSNKELGVDQESEEGKGKTSPDKQKQSPQPQPGSSDQESEEQQQFRNIFKQIAGDDMEICADELKKVLNTVVNKHKDLKTHGF TLESCRSMIALMDTDGSGKLNLQEFHHLWNKIKAWQKIFKHYDTDQSGTINSYEMRNAVNDAGFHLNNQLYDIITMRYADKHMNIDFDSF
P20807-5	MEICADELKKVLNTVVNKHKDLKTHGFTLESCRSMIALMDTDGSGKLNLQEFHHLWNKIKAWQKIFKHYDTDQSGTINSYEMRNAVNDAG

Protein Functional Features

Main function of this protein. (from UniProt)

CAPN3 (go to UniProt):P20807

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
P20807	Domain	74	417	Note=Calpain catalytic;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00239	Type=Deletion;Start=268;End=315
P20807	Domain	74	417	Note=Calpain catalytic;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00239	Type=Deletion;Start=1;End=512
P20807	Domain	74	417	Note=Calpain catalytic;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00239	Type=Deletion;Start=1;End=665
P20807	Domain	649	683	Note=EF-hand 1;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00448	Type=Deletion;Start=1;End=665
P20807	Region	7	37	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=1;End=512
P20807	Region	7	37	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=1;End=665
P20807	Region	418	586	Note=Domain III	Type=Deletion;Start=1;End=512
P20807	Region	418	586	Note=Domain III	Type=Deletion;Start=1;End=665
P20807	Region	587	649	Note=Linker	Type=Deletion;Start=595;End=638
P20807	Region	587	649	Note=Linker	Type=Deletion;Start=595;End=600
P20807	Region	587	649	Note=Linker	Type=Deletion;Start=1;End=665
P20807	Region	609	652	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=595;End=638
P20807	Region	609	652	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=1;End=665
P20807	Region	650	821	Note=Domain IV	Type=Deletion;Start=1;End=665
P20807	Compositional bias	613	630	Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=595;End=638
P20807	Compositional bias	613	630	Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=1;End=665
P20807	Compositional bias	631	652	Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=595;End=638
P20807	Compositional bias	631	652	Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=1;End=665

Gene Isoform Structures and Expression Levels for CAPN3

Gene structures of our canonical and alternative spliced genes of CAPN3
* 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 P20807-1

3D view using mol* of P20807-2

3D view using mol* of P20807-3

3D view using mol* of P20807-4

3D view using mol* of P20807-5

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 P20807-1

pLDDT distribution across the protein length of P20807-2

pLDDT distribution across the protein length of P20807-3

pLDDT distribution across the protein length of P20807-4

pLDDT distribution across the protein length of P20807-5

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 P20807-1

Ramachandran plot of P20807-2

Ramachandran plot of P20807-3

Ramachandran plot of P20807-5

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
P20807-1	1.112	215	1.174	430.122	0.457	0.765	1.022	1.88	0.691	2.719	0.704	588,589,590,602,603,604,605,702,703,704,705,706,70 8,758,762,765,766,769,770,785,788,789,791,792,793, 794,795,796,797,807,812,814,815,816,817,818,819,82 0,821
P20807-2	1.044	220	1.025	570.409	0.455	0.763	1.015	0.635	1.143	0.555	0.695	127,129,130,221,222,223,224,236,237,238,239,240,24 3,245,247,251,265,266,267,268,274,275,285,286,287, 362,364,373,374,433,486,487,488,490,492,495,496,49 7,498
P20807-3	1.092	133	1.116	271.656	0.39	0.809	1.116	1.052	0.95	1.107	1.19	596,597,598,599,600,602,696,697,698,699,700,702,78 2,785,786,788,789,793,807,810,811,814,815
P20807-4	1.03	184	1.058	606.767	0.429	0.72	0.953	0.864	0.962	0.898	0.53	1,3,4,5,7,8,12,13,37,41,42,43,44,45,57,58,59,61,67 ,68,69,70,71,72,73,74,247,248,249
P20807-5	0.941	46	1.006	142.345	0.57	0.718	0.937	2.867	0.191	15.023	0.613	93,97,100,101,104,105,120,123,124,127,128,131

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 P20807-1_P20807-1_6bjd_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 P20807-1_6bjd_A_P20807-2.pdb

3D view using mol* of P20807-1_6bjd_A_P20807-3.pdb

3D view using mol* of P20807-1_6bjd_A_P20807-4.pdb

3D view using mol* of P20807-1_6bjd_A_P20807-5.pdb

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

3D view using mol* of P20807-1_P20807-2.pdb

3D view using mol* of P20807-1_P20807-3.pdb

3D view using mol* of P20807-1_P20807-4.pdb

3D view using mol* of P20807-1_P20807-5.pdb

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

./stats/secondary_structure/figure/P20807-1_vs_P20807-2.png

./stats/secondary_structure/figure/P20807-1_vs_P20807-3.png

./stats/secondary_structure/figure/P20807-1_vs_P20807-4.png

./stats/secondary_structure/figure/P20807-1_vs_P20807-5.png

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

./stats/relative_asa/P20807-1_vs_P20807-2.png

./stats/relative_asa/P20807-1_vs_P20807-3.png

./stats/relative_asa/P20807-1_vs_P20807-4.png

./stats/relative_asa/P20807-1_vs_P20807-5.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 CAPN3

Drugs targeting this gene/protein.
(DrugBank)

UniProt accession	Gene name	DrugBank ID	Drug name	Drug group	Actions
P20807	CAPN3	DB06124	L-aminocarnityl-succinyl-leucyl-argininal-diethylacetal	investigational

Related Diseases to CAPN3

Previous studies relating to the alternative splicing of CAPN3 and disease information from the MeSH term (PubMed)

Gene	PMID	Title	Abstract	MeSH ID	MeSH term
CAPN3	22158424	CAPN3 mRNA processing alteration caused by splicing mutation associated with novel genomic rearrangement of Alu elements.	Recessive mutations of CAPN3 gene are reported to be responsible for limb girdle muscular dystrophy type 2A (LGMD2A). In all, 15-25% of intronic nucleotide changes identified in this gene were investigated by in silico analysis, but occasionally supported by experimental data or reported in some cases as a polymorphism. We report here genetic and transcriptional analyses in three Tunisian patients belonging to the same consanguineous family sharing the same mutation c.1194-9 A>G and Alu repeats insertion in intron 7 of CAPN3 gene. Reverse transcriptase-PCR experiments performed on total RNA from the patient's muscle biopsy showed retention of the eight last nucleotides of intron 9 in the CAPN3 transcript lacking the first seven exons. Our results provide evidence regarding the potential involvement of Alu elements in aberrant processing of pre-mRNA owing to the disruption of pre-existing intronic splicing regulatory elements. We also demonstrated variable mRNA alternative splicing among tissues and between LGMD2A patients. A deep intronic variation and rearrangement have been reported in the literature as causing genetic diseases in humans. However, this is the first report on a potential pathogenic CAPN3 gene mutation resulting from an Alu insertion.	D049288	Muscular Dystrophies, Limb-Girdle

Clinically important variants in CAPN3

(ClinVar, 04/20/2024)

accession_id	uniprot_id	gene_name	Type	Variant	Clinical_significance
P20807	P20807-1	CAPN3	Deletion	p.Ser215_Gly221del	Pathogenic
P20807	P20807-1	CAPN3	Deletion	p.Ser215_Gly221del	Pathogenic