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:MTSS1

Protein Summary

Gene summary

Gene name: MTSS1
ASpdb.0 ID: 9788
	Gene
Gene symbol	MTSS1
Gene ID	9788
Gene name	MTSS I-BAR domain containing 1
Synonyms	MIM\|MIMA\|MIMB
Cytomap	8q24.13
Type of gene	protein-coding
Description	protein MTSS 1MTSS1, I-BAR domain containingmetastasis suppressor 1metastasis suppressor YGL-1metastasis suppressor protein 1missing in metastasis protein
Modification date	20240411
UniProtAcc	O43312

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

Partner	Gene	GO ID	GO term	PubMed ID
Gene	MTSS1	GO:0003785	actin monomer binding	12570871
Gene	MTSS1	GO:0015629	actin cytoskeleton	12570871

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
O43312-1	O43312-1_2d1k_C.pdb	2D1K	X-ray	2.5	C	725	753

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

O43312

MTSS1

O43312-1

O43312-2

755

473

200

Deletion

none

O43312

MTSS1

O43312-1

O43312-2

755

473

345

426

Deletion

none

144

O43312

MTSS1

O43312-1

O43312-4

755

730

346

409

Substitution

LSNGFSHYSLSSESHVGPTGAGLFPHCLPASRLLPRVTSVHLPDYAHYYTIGPGMFPSSQIPSW

NSSSSASSEASETCQSVSECSSPTSVSSGSTMGAWVSTE

346

384

O43312

MTSS1

O43312-1

O43312-5

755

759

153

Substitution

KVDTL

153

157

Multiple sequence alignment of our canonical and alternatively spliced MTSS1

Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of MTSS1

UniProt-id	ENSG	ENST	ENSP
O43312-1	ENSG00000170873.19	ENST00000518547.6	ENSP00000429064.1
O43312-2	ENSG00000170873.19	ENST00000431961.6	ENSP00000393606.2
O43312-4	ENSG00000170873.19	ENST00000378017.7	ENSP00000367256.3
O43312-5	ENSG00000170873.19	ENST00000325064.9	ENSP00000322804.5

UniProt-id	NM ID	NP ID
O43312-1	NM_014751.5	NP_055566.3
O43312-4	NM_001282974.1	NP_001269903.1
O43312-5	NM_001282971.1	NP_001269900.1

Amino acid sequences of our canonical and alternatively spliced MTSS1

accession_id	Protein sequence
O43312-1	MEAVIEKECSALGGLFQTIISDMKGSYPVWEDFINKAGKLQSQLRTTVVAAAAFLDAFQKVADMATNTRGGTREIGSALTRMCMRHRSIE AKLRQFSSALIDCLINPLQEQMEEWKKVANQLDKDHAKEYKKARQEIKKKSSDTLKLQKKAKKGRGDIQPQLDSALQDVNDKYLLLEETE KQAVRKALIEERGRFCTFISMLRPVIEEEISMLGEITHLQTISEDLKSLTMDPHKLPSSSEQVILDLKGSDYSWSYQTPPSSPSTTMSRK SSVCSSLNSVNSSDSRSSGSHSHSPSSHYRYRSSNLAQQAPVRLSSVSSHDSGFISQDAFQSKSPSPMPPEAPNQLSNGFSHYSLSSESH VGPTGAGLFPHCLPASRLLPRVTSVHLPDYAHYYTIGPGMFPSSQIPSWKDWAKPGPYDQPLVNTLQRRKEKREPDPNGGGPTTASGPPA AAEEAQRPRSMTVSAATRPGEEMEACEELALALSRGLQLDTQRSSRDSLQCSSGYSTQTTTPCCSEDTIPSQVSDYDYFSVSGDQEADQQ EFDKSSTIPRNSDISQSYRRMFQAKRPASTAGLPTTLGPAMVTPGVATIRRTPSTKPSVRRGTIGAGPIPIKTPVIPVKTPTVPDLPGVL PAPPDGPEERGEHSPESPSVGEGPQGVTSMPSSMWSGQASVNPPLPGPKPSIPEEHRQAIPESEAEDQEREPPSATVSPGQIPESDPADL
O43312-2	MLRPVIEEEISMLGEITHLQTISEDLKSLTMDPHKLPSSSEQVILDLKGSDYSWSYQTPPSSPSTTMSRKSSVCSSLNSVNSSDSRSSGS HSHSPSSHYRYRSSNLAQQAPVRLSSVSSHDSGFISQDAFQSKSPSPMPPEAPNQRRKEKREPDPNGGGPTTASGPPAAAEEAQRPRSMT VSAATRPGEEMEACEELALALSRGLQLDTQRSSRDSLQCSSGYSTQTTTPCCSEDTIPSQVSDYDYFSVSGDQEADQQEFDKSSTIPRNS DISQSYRRMFQAKRPASTAGLPTTLGPAMVTPGVATIRRTPSTKPSVRRGTIGAGPIPIKTPVIPVKTPTVPDLPGVLPAPPDGPEERGE HSPESPSVGEGPQGVTSMPSSMWSGQASVNPPLPGPKPSIPEEHRQAIPESEAEDQEREPPSATVSPGQIPESDPADLSPRDTPQGEDML
O43312-4	MEAVIEKECSALGGLFQTIISDMKGSYPVWEDFINKAGKLQSQLRTTVVAAAAFLDAFQKVADMATNTRGGTREIGSALTRMCMRHRSIE AKLRQFSSALIDCLINPLQEQMEEWKKVANQLDKDHAKEYKKARQEIKKKSSDTLKLQKKAKKGRGDIQPQLDSALQDVNDKYLLLEETE KQAVRKALIEERGRFCTFISMLRPVIEEEISMLGEITHLQTISEDLKSLTMDPHKLPSSSEQVILDLKGSDYSWSYQTPPSSPSTTMSRK SSVCSSLNSVNSSDSRSSGSHSHSPSSHYRYRSSNLAQQAPVRLSSVSSHDSGFISQDAFQSKSPSPMPPEAPNQNSSSSASSEASETCQ SVSECSSPTSVSSGSTMGAWVSTEKDWAKPGPYDQPLVNTLQRRKEKREPDPNGGGPTTASGPPAAAEEAQRPRSMTVSAATRPGEEMEA CEELALALSRGLQLDTQRSSRDSLQCSSGYSTQTTTPCCSEDTIPSQVSDYDYFSVSGDQEADQQEFDKSSTIPRNSDISQSYRRMFQAK RPASTAGLPTTLGPAMVTPGVATIRRTPSTKPSVRRGTIGAGPIPIKTPVIPVKTPTVPDLPGVLPAPPDGPEERGEHSPESPSVGEGPQ GVTSMPSSMWSGQASVNPPLPGPKPSIPEEHRQAIPESEAEDQEREPPSATVSPGQIPESDPADLSPRDTPQGEDMLNAIRRGVKLKKTT
O43312-5	MEAVIEKECSALGGLFQTIISDMKGSYPVWEDFINKAGKLQSQLRTTVVAAAAFLDAFQKVADMATNTRGGTREIGSALTRMCMRHRSIE AKLRQFSSALIDCLINPLQEQMEEWKKVANQLDKDHAKEYKKARQEIKKKSSDTLKLQKKAKKVDTLGRGDIQPQLDSALQDVNDKYLLL EETEKQAVRKALIEERGRFCTFISMLRPVIEEEISMLGEITHLQTISEDLKSLTMDPHKLPSSSEQVILDLKGSDYSWSYQTPPSSPSTT MSRKSSVCSSLNSVNSSDSRSSGSHSHSPSSHYRYRSSNLAQQAPVRLSSVSSHDSGFISQDAFQSKSPSPMPPEAPNQLSNGFSHYSLS SESHVGPTGAGLFPHCLPASRLLPRVTSVHLPDYAHYYTIGPGMFPSSQIPSWKDWAKPGPYDQPLVNTLQRRKEKREPDPNGGGPTTAS GPPAAAEEAQRPRSMTVSAATRPGEEMEACEELALALSRGLQLDTQRSSRDSLQCSSGYSTQTTTPCCSEDTIPSQVSDYDYFSVSGDQE ADQQEFDKSSTIPRNSDISQSYRRMFQAKRPASTAGLPTTLGPAMVTPGVATIRRTPSTKPSVRRGTIGAGPIPIKTPVIPVKTPTVPDL PGVLPAPPDGPEERGEHSPESPSVGEGPQGVTSMPSSMWSGQASVNPPLPGPKPSIPEEHRQAIPESEAEDQEREPPSATVSPGQIPESD

Protein Functional Features

Main function of this protein. (from UniProt)

MTSS1 (go to UniProt):O43312

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
O43312	Domain	1	250	Note=IMD;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00668	Type=Deletion;Start=1;End=200
O43312	Domain	1	250	Note=IMD;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00668	Type=Substitution;Start=153;End=153
O43312	Region	139	159	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=1;End=200
O43312	Region	139	159	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Substitution;Start=153;End=153
O43312	Region	327	351	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=345;End=426
O43312	Region	327	351	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Substitution;Start=346;End=409
O43312	Coiled coil	108	155	Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Deletion;Start=1;End=200
O43312	Coiled coil	108	155	Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Substitution;Start=153;End=153
O43312	Compositional bias	139	157	Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=1;End=200
O43312	Compositional bias	139	157	Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Substitution;Start=153;End=153

Gene Isoform Structures and Expression Levels for MTSS1

Gene structures of our canonical and alternative spliced genes of MTSS1
* 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 O43312-1

3D view using mol* of O43312-2

3D view using mol* of O43312-4

3D view using mol* of O43312-5

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 O43312-1

pLDDT distribution across the protein length of O43312-2

pLDDT distribution across the protein length of O43312-4

pLDDT distribution across the protein length of O43312-5

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 O43312-1

Ramachandran plot of O43312-2

Ramachandran plot of O43312-4

Ramachandran plot of O43312-5

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
O43312-1	0.815	50	0.808	117.649	0.612	0.672	0.937	0.791	0.796	0.993	0.947	16,122,125,126,129,132,133,136,175,178,179,182,183 ,186
O43312-2	0.554	22	0.492	61.74	0.728	0.569	0.835	0.501	0.89	0.563	7.886	28,29,31,32,35,36,37
O43312-4	0.805	49	0.793	116.62	0.598	0.672	0.961	1.091	0.822	1.328	0.602	16,122,125,126,129,132,133,175,179,182,183,186
O43312-5	0.827	55	0.852	121.422	0.645	0.609	0.843	1.22	0.644	1.894	0.944	16,118,121,122,125,126,129,132,133,136,137,176,179 ,182,183,186,187,190

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 O43312-1_O43312-1_2d1k_C.pdb

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

3D view using mol* of O43312-1_2d1k_C_O43312-2.pdb

3D view using mol* of O43312-1_2d1k_C_O43312-4.pdb

3D view using mol* of O43312-1_2d1k_C_O43312-5.pdb

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

3D view using mol* of O43312-1_O43312-2.pdb

3D view using mol* of O43312-1_O43312-4.pdb

3D view using mol* of O43312-1_O43312-5.pdb

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

./stats/secondary_structure/figure/O43312-1_vs_O43312-2.png

./stats/secondary_structure/figure/O43312-1_vs_O43312-4.png

./stats/secondary_structure/figure/O43312-1_vs_O43312-5.png

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

./stats/relative_asa/O43312-1_vs_O43312-2.png

./stats/relative_asa/O43312-1_vs_O43312-4.png

./stats/relative_asa/O43312-1_vs_O43312-5.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 MTSS1

Drugs targeting this gene/protein.
(DrugBank)

UniProt accession

Gene name

DrugBank ID

Drug name

Drug group

Actions

Related Diseases to MTSS1

Previous studies relating to the alternative splicing of MTSS1 and disease information from the MeSH term (PubMed)

Gene

PMID

Title

Abstract

MeSH ID

MeSH term

Clinically important variants in MTSS1

(ClinVar, 04/20/2024)

accession_id

uniprot_id

gene_name

Type

Variant

Clinical_significance