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:HSF1

Protein Summary

Gene summary

Gene name: HSF1
ASpdb.0 ID: 3297
	Gene
Gene symbol	HSF1
Gene ID	3297
Gene name	heat shock transcription factor 1
Synonyms	HSTF1
Cytomap	8q24.3
Type of gene	protein-coding
Description	heat shock factor protein 1
Modification date	20240411
UniProtAcc	Q00613

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

Partner	Gene	GO ID	GO term	PubMed ID
Gene	HSF1	GO:0000122	negative regulation of transcription by RNA polymerase II	8926278\|9341107
Gene	HSF1	GO:0000165	MAPK cascade	12917326
Gene	HSF1	GO:0000776	kinetochore	18794143
Gene	HSF1	GO:0000976	transcription cis-regulatory region binding	24504023
Gene	HSF1	GO:0000978	RNA polymerase II cis-regulatory region sequence-specific DNA binding	8926278\|8972228
Gene	HSF1	GO:0000981	DNA-binding transcription factor activity, RNA polymerase II-specific	24504023
Gene	HSF1	GO:0001162	RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding	10561509
Gene	HSF1	GO:0001227	DNA-binding transcription repressor activity, RNA polymerase II-specific	8926278
Gene	HSF1	GO:0001228	DNA-binding transcription activator activity, RNA polymerase II-specific	7760831\|25963659
Gene	HSF1	GO:0003677	DNA binding	7935471\|8455624\|9222587\|9341107\|9499401\|9727490\|10359787\|10413683\|10747973\|11514557\|11583998\|12659875\|12665592\|12917326\|16278218\|16554823\|26754925
Gene	HSF1	GO:0005634	nucleus	8455624\|9341107\|10413683\|10747973\|12665592\|12917326\|14707147\|21085490\|25963659\|26159920
Gene	HSF1	GO:0005654	nucleoplasm	10359787
Gene	HSF1	GO:0005737	cytoplasm	8455624\|10413683\|10747973\|12917326\|21085490\|26159920
Gene	HSF1	GO:0005813	centrosome	18794143
Gene	HSF1	GO:0005829	cytosol	-
Gene	HSF1	GO:0006357	regulation of transcription by RNA polymerase II	7760831
Gene	HSF1	GO:0016605	PML body	11514557
Gene	HSF1	GO:0031072	heat shock protein binding	9727490\|11583998\|16278218
Gene	HSF1	GO:0031490	chromatin DNA binding	21085490
Gene	HSF1	GO:0034605	cellular response to heat	7760831\|7935471\|9222587\|9341107\|9499401\|10359787\|10413683\|10747973\|11514557\|11583998\|12659875\|12665592\|12917326\|14707147\|16554823\|17897941\|21085490\|26159920
Gene	HSF1	GO:0034620	cellular response to unfolded protein	15016915
Gene	HSF1	GO:0042802	identical protein binding	7935471\|9222587\|9727490\|11583998\|16554823\|26754925
Gene	HSF1	GO:0043565	sequence-specific DNA binding	25963659
Gene	HSF1	GO:0045944	positive regulation of transcription by RNA polymerase II	10561509
Gene	HSF1	GO:0045944	positive regulation of transcription by RNA polymerase II	9341107\|9499401\|10747973\|11514557\|12659875\|12665592\|12917326\|15016915\|16278218\|21085490\|21597468\|24504023\|25963659\|26754925
Gene	HSF1	GO:0046982	protein heterodimerization activity	9222587
Gene	HSF1	GO:0048471	perinuclear region of cytoplasm	21085490
Gene	HSF1	GO:0051879	Hsp90 protein binding	11583998
Gene	HSF1	GO:0061770	translation elongation factor binding	16554823
Gene	HSF1	GO:0065003	protein-containing complex assembly	11583998
Gene	HSF1	GO:0071276	cellular response to cadmium ion	10359787\|11514557\|15016915
Gene	HSF1	GO:0071280	cellular response to copper ion	15016915
Gene	HSF1	GO:0071480	cellular response to gamma radiation	26359349
Gene	HSF1	GO:0072738	cellular response to diamide	15016915
Gene	HSF1	GO:0097165	nuclear stress granule	10359787\|10747973\|11514557\|12665592\|14707147\|25963659
Gene	HSF1	GO:0097431	mitotic spindle pole	18794143
Gene	HSF1	GO:0101031	protein folding chaperone complex	8455624
Gene	HSF1	GO:1900034	regulation of cellular response to heat	11583998
Gene	HSF1	GO:1903936	cellular response to sodium arsenite	15016915
Gene	HSF1	GO:1990837	sequence-specific double-stranded DNA binding	28473536
Gene	HSF1	GO:1990904	ribonucleoprotein complex	16554823

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
Q00613-1	Q00613-1_5d5v_D.pdb	5D5V	X-ray	2.55	D	13	120

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

Q00613

HSF1

Q00613-1

Q00613-2

529

489

462

489

Substitution

GKQLVHYTAQPLFLLDPGSVDTGSNDLP

AGALHSAAAVPAGPRLRGHREQRPAGAV

462

489

Q00613

HSF1

Q00613-1

Q00613-2

529

489

490

529

Deletion

none

489

Multiple sequence alignment of our canonical and alternatively spliced HSF1

Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of HSF1

UniProt-id	ENSG	ENST	ENSP
Q00613-1	ENSG00000185122.11	ENST00000528838.6	ENSP00000431512.1
Q00613-1	ENSG00000284774.2	ENST00000646252.2	ENSP00000493830.1

UniProt-id	NM ID	NP ID
Q00613-1	NM_005526.3	NP_005517.1
Q00613-2	XM_017013377.1	XP_016868866.1

Amino acid sequences of our canonical and alternatively spliced HSF1

accession_id	Protein sequence
Q00613-1	MDLPVGPGAAGPSNVPAFLTKLWTLVSDPDTDALICWSPSGNSFHVFDQGQFAKEVLPKYFKHNNMASFVRQLNMYGFRKVVHIEQGGLV KPERDDTEFQHPCFLRGQEQLLENIKRKVTSVSTLKSEDIKIRQDSVTKLLTDVQLMKGKQECMDSKLLAMKHENEALWREVASLRQKHA QQQKVVNKLIQFLISLVQSNRILGVKRKIPLMLNDSGSAHSMPKYSRQFSLEHVHGSGPYSAPSPAYSSSSLYAPDAVASSGPIISDITE LAPASPMASPGGSIDERPLSSSPLVRVKEEPPSPPQSPRVEEASPGRPSSVDTLLSPTALIDSILRESEPAPASVTALTDARGHTDTEGR PPSPPPTSTPEKCLSVACLDKNELSDHLDAMDSNLDNLQTMLSSHGFSVDTSALLDLFSPSVTVPDMSLPDLDSSLASIQELLSPQEPPR
Q00613-2	MDLPVGPGAAGPSNVPAFLTKLWTLVSDPDTDALICWSPSGNSFHVFDQGQFAKEVLPKYFKHNNMASFVRQLNMYGFRKVVHIEQGGLV KPERDDTEFQHPCFLRGQEQLLENIKRKVTSVSTLKSEDIKIRQDSVTKLLTDVQLMKGKQECMDSKLLAMKHENEALWREVASLRQKHA QQQKVVNKLIQFLISLVQSNRILGVKRKIPLMLNDSGSAHSMPKYSRQFSLEHVHGSGPYSAPSPAYSSSSLYAPDAVASSGPIISDITE LAPASPMASPGGSIDERPLSSSPLVRVKEEPPSPPQSPRVEEASPGRPSSVDTLLSPTALIDSILRESEPAPASVTALTDARGHTDTEGR PPSPPPTSTPEKCLSVACLDKNELSDHLDAMDSNLDNLQTMLSSHGFSVDTSALLDLFSPSVTVPDMSLPDLDSSLASIQELLSPQEPPR

Protein Functional Features

Main function of this protein. (from UniProt)

HSF1 (go to UniProt):Q00613

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
Q00613	Region	371	529	"Note=Transactivation domain;Ontology_term=ECO:0000269	ECO:0000269;evidence=ECO:0000269\|PubMed:7623826
Q00613	Region	371	529	"Note=Transactivation domain;Ontology_term=ECO:0000269	ECO:0000269;evidence=ECO:0000269\|PubMed:7623826
Q00613	Region	444	463	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Substitution;Start=462;End=489
Q00613	Region	502	529	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=490;End=529

Gene Isoform Structures and Expression Levels for HSF1

Gene structures of our canonical and alternative spliced genes of HSF1
* 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 Q00613-1

3D view using mol* of Q00613-2

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 Q00613-1

pLDDT distribution across the protein length of Q00613-2

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 Q00613-1

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
Q00613-1	0.677	35	0.59	140.287	0.682	0.662	0.809	0.058	1.116	0.052	0.723	80,81,82,83,86,92,96,97,98
Q00613-2	0.983	73	1.066	190.022	0.628	0.64	0.848	1.816	0.371	4.891	1.259	162,165,166,169,170,172,173,176,433,436,439,440,44 3

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 Q00613-1_Q00613-1_5d5v_D.pdb

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

3D view using mol* of Q00613-1_5d5v_D_Q00613-2.pdb

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

3D view using mol* of Q00613-1_Q00613-2.pdb

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

./stats/secondary_structure/figure/Q00613-1_vs_Q00613-2.png

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

./stats/relative_asa/Q00613-1_vs_Q00613-2.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 HSF1

Drugs targeting this gene/protein.
(DrugBank)

UniProt accession	Gene name	DrugBank ID	Drug name	Drug group	Actions
Q00613	HSF1	DB06258	Bimoclomol	investigational

Related Diseases to HSF1

Previous studies relating to the alternative splicing of HSF1 and disease information from the MeSH term (PubMed)

Gene

PMID

Title

Abstract

MeSH ID

MeSH term

Clinically important variants in HSF1

(ClinVar, 04/20/2024)

accession_id

uniprot_id

gene_name

Type

Variant

Clinical_significance