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:PDS5B

Protein Summary

Gene summary

Gene name: PDS5B
ASpdb.0 ID: 23047
	Gene
Gene symbol	PDS5B
Gene ID	23047
Gene name	PDS5 cohesin associated factor B
Synonyms	APRIN\|AS3\|CG008
Cytomap	13q13.1
Type of gene	protein-coding
Description	sister chromatid cohesion protein PDS5 homolog Bandrogen induced inhibitor of proliferationandrogen-induced proliferation inhibitorandrogen-induced prostate proliferative shutoff-associated protein AS3androgen-induced shutoff 3
Modification date	20240407
UniProtAcc	Q9NTI5

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

Partner	Gene	GO ID	GO term	PubMed ID
Gene	PDS5B	GO:0000785	chromatin	16682347
Gene	PDS5B	GO:0003677	DNA binding	19412548
Gene	PDS5B	GO:0005654	nucleoplasm	-
Gene	PDS5B	GO:0008285	negative regulation of cell population proliferation	10963680
Gene	PDS5B	GO:0042127	regulation of cell population proliferation	10963680

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
Q9NTI5-1	Q9NTI5-1_5hdt_B.pdb	5HDT	X-ray	2.71	B	21	1120

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

Q9NTI5

PDS5B

Q9NTI5-1

Q9NTI5-3

1447

529

491

529

Substitution

ALNEMWKCQNLLRHQVKDLLDLIKQPKTDASVKAIFSKV

YVSNIKFCSFHPLQYIGFYGKETTNTCILKCNLCSVNIV

491

529

Q9NTI5

PDS5B

Q9NTI5-1

Q9NTI5-3

1447

529

530

1447

Deletion

none

529

Q9NTI5

PDS5B

Q9NTI5-1

Q9NTI5-4

1447

122

105

122

Substitution

DIFMFITRQLKGLEDTKS

ASTDLNNSKIDRYFDLSF

105

122

Q9NTI5

PDS5B

Q9NTI5-1

Q9NTI5-4

1447

122

123

1447

Deletion

none

122

Q9NTI5

PDS5B

Q9NTI5-1

Q9NTI5-5

1447

125

1230

Deletion

none

Q9NTI5

PDS5B

Q9NTI5-1

Q9NTI5-5

1447

125

1356

1447

Deletion

none

125

Multiple sequence alignment of our canonical and alternatively spliced PDS5B

Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of PDS5B

UniProt-id	ENSG	ENST	ENSP
Q9NTI5-1	ENSG00000083642.19	ENST00000315596.15	ENSP00000313851.10

UniProt-id	NM ID	NP ID
Q9NTI5-1	NM_015032.3	NP_055847.1

Amino acid sequences of our canonical and alternatively spliced PDS5B

accession_id	Protein sequence
Q9NTI5-1	MAHSKTRTNDGKITYPPGVKEISDKISKEEMVRRLKMVVKTFMDMDQDSEEEKELYLNLALHLASDFFLKHPDKDVRLLVACCLADIFRI YAPEAPYTSPDKLKDIFMFITRQLKGLEDTKSPQFNRYFYLLENIAWVKSYNICFELEDSNEIFTQLYRTLFSVINNGHNQKVHMHMVDL MSSIICEGDTVSQELLDTVLVNLVPAHKNLNKQAYDLAKALLKRTAQAIEPYITNFFNQVLMLGKTSISDLSEHVFDLILELYNIDSHLL LSVLPQLEFKLKSNDNEERLQVVKLLAKMFGAKDSELASQNKPLWQCYLGRFNDIHVPIRLECVKFASHCLMNHPDLAKDLTEYLKVRSH DPEEAIRHDVIVSIVTAAKKDILLVNDHLLNFVRERTLDKRWRVRKEAMMGLAQIYKKYALQSAAGKDAAKQIAWIKDKLLHIYYQNSID DRLLVERIFAQYMVPHNLETTERMKCLYYLYATLDLNAVKALNEMWKCQNLLRHQVKDLLDLIKQPKTDASVKAIFSKVMVITRNLPDPG KAQDFMKKFTQVLEDDEKIRKQLEVLVSPTCSCKQAEGCVREITKKLGNPKQPTNPFLEMIKFLLERIAPVHIDTESISALIKQVNKSID GTADDEDEGVPTDQAIRAGLELLKVLSFTHPISFHSAETFESLLACLKMDDEKVAEAALQIFKNTGSKIEEDFPHIRSALLPVLHHKSKK GPPRQAKYAIHCIHAIFSSKETQFAQIFEPLHKSLDPSNLEHLITPLVTIGHIALLAPDQFAAPLKSLVATFIVKDLLMNDRLPGKKTTK LWVPDEEVSPETMVKIQAIKMMVRWLLGMKNNHSKSGTSTLRLLTTILHSDGDLTEQGKISKPDMSRLRLAAGSAIVKLAQEPCYHEIIT LEQYQLCALAINDECYQVRQVFAQKLHKGLSRLRLPLEYMAICALCAKDPVKERRAHARQCLVKNINVRREYLKQHAAVSEKLLSLLPEY VVPYTIHLLAHDPDYVKVQDIEQLKDVKECLWFVLEILMAKNENNSHAFIRKMVENIKQTKDAQGPDDAKMNEKLYTVCDVAMNIIMSKS TTYSLESPKDPVLPARFFTQPDKNFSNTKNYLPPEMKSFFTPGKPKTTNVLGAVNKPLSSAGKQSQTKSSRMETVSNASSSSNPSSPGRI KGRLDSSEMDHSENEDYTMSSPLPGKKSDKRDDSDLVRSELEKPRGRKKTPVTEQEEKLGMDDLTKLVQEQKPKGSQRSRKRGHTASESD EQQWPEEKRLKEDILENEDEQNSPPKKGKRGRPPKPLGGGTPKEEPTMKTSKKGSKKKSGPPAPEEEEEEERQSGNTEQKSKSKQHRVSR RAQQRAESPESSAIESTQSTPQKGRGRPSKTPSPSQPKKNVRVGRSKQAATKENDSSEEVDVFQGSSPVDDIPQEETEEEEVSTVNVRRR
Q9NTI5-3	MAHSKTRTNDGKITYPPGVKEISDKISKEEMVRRLKMVVKTFMDMDQDSEEEKELYLNLALHLASDFFLKHPDKDVRLLVACCLADIFRI YAPEAPYTSPDKLKDIFMFITRQLKGLEDTKSPQFNRYFYLLENIAWVKSYNICFELEDSNEIFTQLYRTLFSVINNGHNQKVHMHMVDL MSSIICEGDTVSQELLDTVLVNLVPAHKNLNKQAYDLAKALLKRTAQAIEPYITNFFNQVLMLGKTSISDLSEHVFDLILELYNIDSHLL LSVLPQLEFKLKSNDNEERLQVVKLLAKMFGAKDSELASQNKPLWQCYLGRFNDIHVPIRLECVKFASHCLMNHPDLAKDLTEYLKVRSH DPEEAIRHDVIVSIVTAAKKDILLVNDHLLNFVRERTLDKRWRVRKEAMMGLAQIYKKYALQSAAGKDAAKQIAWIKDKLLHIYYQNSID
Q9NTI5-4	MAHSKTRTNDGKITYPPGVKEISDKISKEEMVRRLKMVVKTFMDMDQDSEEEKELYLNLALHLASDFFLKHPDKDVRLLVACCLADIFRI
Q9NTI5-5	MDDLTKLVQEQKPKGSQRSRKRGHTASESDEQQWPEEKRLKEDILENEDEQNSPPKKGKRGRPPKPLGGGTPKEEPTMKTSKKGSKKKSG

Protein Functional Features

Main function of this protein. (from UniProt)

PDS5B (go to UniProt):Q9NTI5

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
Q9NTI5	Repeat	383	419	Note=HEAT;Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Deletion;Start=123;End=1447
Q9NTI5	Repeat	383	419	Note=HEAT;Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Deletion;Start=1;End=1230
Q9NTI5	DNA binding	1249	1261	Note=A.T hook 1;Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Deletion;Start=530;End=1447
Q9NTI5	DNA binding	1249	1261	Note=A.T hook 1;Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Deletion;Start=123;End=1447
Q9NTI5	DNA binding	1287	1299	Note=A.T hook 2;Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Deletion;Start=530;End=1447
Q9NTI5	DNA binding	1287	1299	Note=A.T hook 2;Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Deletion;Start=123;End=1447
Q9NTI5	DNA binding	1372	1384	Note=A.T hook 3;Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Deletion;Start=530;End=1447
Q9NTI5	DNA binding	1372	1384	Note=A.T hook 3;Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Deletion;Start=123;End=1447
Q9NTI5	DNA binding	1372	1384	Note=A.T hook 3;Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Deletion;Start=1356;End=1447
Q9NTI5	Region	1117	1447	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=530;End=1447
Q9NTI5	Region	1117	1447	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=123;End=1447
Q9NTI5	Region	1117	1447	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=1;End=1230
Q9NTI5	Region	1117	1447	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=1356;End=1447
Q9NTI5	Compositional bias	1132	1170	Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=530;End=1447
Q9NTI5	Compositional bias	1132	1170	Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=123;End=1447
Q9NTI5	Compositional bias	1132	1170	Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=1;End=1230
Q9NTI5	Compositional bias	1195	1287	Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=530;End=1447
Q9NTI5	Compositional bias	1195	1287	Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=123;End=1447
Q9NTI5	Compositional bias	1195	1287	Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=1;End=1230
Q9NTI5	Compositional bias	1306	1325	Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=530;End=1447
Q9NTI5	Compositional bias	1306	1325	Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=123;End=1447
Q9NTI5	Compositional bias	1355	1392	Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=530;End=1447
Q9NTI5	Compositional bias	1355	1392	Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=123;End=1447
Q9NTI5	Compositional bias	1355	1392	Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=1356;End=1447

Gene Isoform Structures and Expression Levels for PDS5B

Gene structures of our canonical and alternative spliced genes of PDS5B
* 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 Q9NTI5-1

3D view using mol* of Q9NTI5-3

3D view using mol* of Q9NTI5-4

3D view using mol* of Q9NTI5-5

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 Q9NTI5-1

pLDDT distribution across the protein length of Q9NTI5-3

pLDDT distribution across the protein length of Q9NTI5-4

pLDDT distribution across the protein length of Q9NTI5-5

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 Q9NTI5-1

Ramachandran plot of Q9NTI5-5

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
Q9NTI5-1	1.103	146	1.141	305.613	0.513	0.797	0.988	1.603	0.85	1.886	0.788	453,454,456,457,459,460,461,466,473,495,496,499,50 0,503,573,574,576,577,580,581,603,606,607,608,609, 610,611,612,613,660
Q9NTI5-3	1.091	120	1.142	305.956	0.506	0.759	1.028	1.297	0.778	1.667	0.92	456,459,460,464,466,473,474,477,478,481,492,495,49 6,499,519,520,521,523,524,526,528
Q9NTI5-4	0.947	53	0.986	290.178	0.576	0.748	0.981	1.609	0.452	3.563	4.225	60,61,64,69,84,87,88,97,114,117,118,121,122
Q9NTI5-5	0.409	17	0.226	9.604	0.767	0.459	0.716	0.019	1.34	0.014	0.302	98,99,100,101,102

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 Q9NTI5-1_Q9NTI5-1_5hdt_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 Q9NTI5-1_5hdt_B_Q9NTI5-3.pdb

3D view using mol* of Q9NTI5-1_5hdt_B_Q9NTI5-4.pdb

3D view using mol* of Q9NTI5-1_5hdt_B_Q9NTI5-5.pdb

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

3D view using mol* of Q9NTI5-1_Q9NTI5-3.pdb

3D view using mol* of Q9NTI5-1_Q9NTI5-4.pdb

3D view using mol* of Q9NTI5-1_Q9NTI5-5.pdb

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

./stats/secondary_structure/figure/Q9NTI5-1_vs_Q9NTI5-3.png

./stats/secondary_structure/figure/Q9NTI5-1_vs_Q9NTI5-4.png

./stats/secondary_structure/figure/Q9NTI5-1_vs_Q9NTI5-5.png

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

./stats/relative_asa/Q9NTI5-1_vs_Q9NTI5-3.png

./stats/relative_asa/Q9NTI5-1_vs_Q9NTI5-4.png

./stats/relative_asa/Q9NTI5-1_vs_Q9NTI5-5.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 PDS5B

Drugs targeting this gene/protein.
(DrugBank)

UniProt accession

Gene name

DrugBank ID

Drug name

Drug group

Actions

Related Diseases to PDS5B

Previous studies relating to the alternative splicing of PDS5B and disease information from the MeSH term (PubMed)

Gene	PMID	Title	Abstract	MeSH ID	MeSH term
PDS5B	24711643	Identifying biological pathways that underlie primordial short stature using network analysis.	Mutations in CUL7, OBSL1 and CCDC8, leading to disordered ubiquitination, cause one of the commonest primordial growth disorders, 3-M syndrome. This condition is associated with i) abnormal p53 function, ii) GH and/or IGF1 resistance, which may relate to failure to recycle signalling molecules, and iii) cellular IGF2 deficiency. However the exact molecular mechanisms that may link these abnormalities generating growth restriction remain undefined. In this study, we have used immunoprecipitation/mass spectrometry and transcriptomic studies to generate a 3-M 'interactome', to define key cellular pathways and biological functions associated with growth failure seen in 3-M. We identified 189 proteins which interacted with CUL7, OBSL1 and CCDC8, from which a network including 176 of these proteins was generated. To strengthen the association to 3-M syndrome, these proteins were compared with an inferred network generated from the genes that were differentially expressed in 3-M fibroblasts compared with controls. This resulted in a final 3-M network of 131 proteins, with the most significant biological pathway within the network being mRNA splicing/processing. We have shown using an exogenous insulin receptor (INSR) minigene system that alternative splicing of exon 11 is significantly changed in HEK293 cells with altered expression of CUL7, OBSL1 and CCDC8 and in 3-M fibroblasts. The net result is a reduction in the expression of the mitogenic INSR isoform in 3-M syndrome. From these preliminary data, we hypothesise that disordered ubiquitination could result in aberrant mRNA splicing in 3-M; however, further investigation is required to determine whether this contributes to growth failure.	D004392	Dwarfism
PDS5B	24711643	Identifying biological pathways that underlie primordial short stature using network analysis.	Mutations in CUL7, OBSL1 and CCDC8, leading to disordered ubiquitination, cause one of the commonest primordial growth disorders, 3-M syndrome. This condition is associated with i) abnormal p53 function, ii) GH and/or IGF1 resistance, which may relate to failure to recycle signalling molecules, and iii) cellular IGF2 deficiency. However the exact molecular mechanisms that may link these abnormalities generating growth restriction remain undefined. In this study, we have used immunoprecipitation/mass spectrometry and transcriptomic studies to generate a 3-M 'interactome', to define key cellular pathways and biological functions associated with growth failure seen in 3-M. We identified 189 proteins which interacted with CUL7, OBSL1 and CCDC8, from which a network including 176 of these proteins was generated. To strengthen the association to 3-M syndrome, these proteins were compared with an inferred network generated from the genes that were differentially expressed in 3-M fibroblasts compared with controls. This resulted in a final 3-M network of 131 proteins, with the most significant biological pathway within the network being mRNA splicing/processing. We have shown using an exogenous insulin receptor (INSR) minigene system that alternative splicing of exon 11 is significantly changed in HEK293 cells with altered expression of CUL7, OBSL1 and CCDC8 and in 3-M fibroblasts. The net result is a reduction in the expression of the mitogenic INSR isoform in 3-M syndrome. From these preliminary data, we hypothesise that disordered ubiquitination could result in aberrant mRNA splicing in 3-M; however, further investigation is required to determine whether this contributes to growth failure.	D006130	Growth Disorders
PDS5B	24711643	Identifying biological pathways that underlie primordial short stature using network analysis.	Mutations in CUL7, OBSL1 and CCDC8, leading to disordered ubiquitination, cause one of the commonest primordial growth disorders, 3-M syndrome. This condition is associated with i) abnormal p53 function, ii) GH and/or IGF1 resistance, which may relate to failure to recycle signalling molecules, and iii) cellular IGF2 deficiency. However the exact molecular mechanisms that may link these abnormalities generating growth restriction remain undefined. In this study, we have used immunoprecipitation/mass spectrometry and transcriptomic studies to generate a 3-M 'interactome', to define key cellular pathways and biological functions associated with growth failure seen in 3-M. We identified 189 proteins which interacted with CUL7, OBSL1 and CCDC8, from which a network including 176 of these proteins was generated. To strengthen the association to 3-M syndrome, these proteins were compared with an inferred network generated from the genes that were differentially expressed in 3-M fibroblasts compared with controls. This resulted in a final 3-M network of 131 proteins, with the most significant biological pathway within the network being mRNA splicing/processing. We have shown using an exogenous insulin receptor (INSR) minigene system that alternative splicing of exon 11 is significantly changed in HEK293 cells with altered expression of CUL7, OBSL1 and CCDC8 and in 3-M fibroblasts. The net result is a reduction in the expression of the mitogenic INSR isoform in 3-M syndrome. From these preliminary data, we hypothesise that disordered ubiquitination could result in aberrant mRNA splicing in 3-M; however, further investigation is required to determine whether this contributes to growth failure.	D009123	Muscle Hypotonia

Clinically important variants in PDS5B

(ClinVar, 04/20/2024)

accession_id

uniprot_id

gene_name

Type

Variant

Clinical_significance