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:GGA3

Protein Summary

Gene summary

Gene name: GGA3
ASpdb.0 ID: 23163
	Gene
Gene symbol	GGA3
Gene ID	23163
Gene name	golgi associated, gamma adaptin ear containing, ARF binding protein 3
Synonyms	-
Cytomap	17q25.1
Type of gene	protein-coding
Description	ADP-ribosylation factor-binding protein GGA3Golgi-localized, gamma ear-containing, ARF-binding protein 3
Modification date	20240411
UniProtAcc	Q9NZ52

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

Partner	Gene	GO ID	GO term	PubMed ID
Gene	GGA3	GO:0005764	lysosome	17116753
Gene	GGA3	GO:0005794	Golgi apparatus	-
Gene	GGA3	GO:0005802	trans-Golgi network	10749927
Gene	GGA3	GO:0031267	small GTPase binding	10749927
Gene	GGA3	GO:0031647	regulation of protein stability	17553422\|20484053
Gene	GGA3	GO:0031648	protein destabilization	20484053
Gene	GGA3	GO:0032991	protein-containing complex	17116753
Gene	GGA3	GO:0043130	ubiquitin binding	17116753\|20484053
Gene	GGA3	GO:0044877	protein-containing complex binding	17116753
Gene	GGA3	GO:1902430	negative regulation of amyloid-beta formation	17553422

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
Q9NZ52-1	Q9NZ52-1_1lf8_B.pdb	1LF8	X-ray	2.3	B	1	157

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

Q9NZ52

GGA3

Q9NZ52-1

Q9NZ52-2

723

690

100

Deletion

none

Q9NZ52

GGA3

Q9NZ52-1

Q9NZ52-3

723

592

122

Deletion

none

Q9NZ52

GGA3

Q9NZ52-1

Q9NZ52-3

723

592

688

723

Substitution

EKVRLRYKLTFALGEQLSTEVGEVDQFPPVEQWGNL

KQVLSFLGKACLQPWGQAILLTTSCLA

566

592

Q9NZ52

GGA3

Q9NZ52-1

Q9NZ52-4

723

651

Deletion

none

Multiple sequence alignment of our canonical and alternatively spliced GGA3

Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of GGA3

UniProt-id	ENSG	ENST	ENSP
Q9NZ52-1	ENSG00000125447.18	ENST00000537686.6	ENSP00000438085.3
Q9NZ52-1	ENSG00000125447.18	ENST00000649398.1	ENSP00000496890.1
Q9NZ52-2	ENSG00000125447.18	ENST00000538886.5	ENSP00000446421.2
Q9NZ52-3	ENSG00000125447.18	ENST00000578348.5	ENSP00000463288.1
Q9NZ52-4	ENSG00000125447.18	ENST00000582717.5	ENSP00000462081.1

UniProt-id	NM ID	NP ID
Q9NZ52-1	NM_138619.3	NP_619525.1
Q9NZ52-2	NM_014001.4	NP_054720.1
Q9NZ52-3	NM_001172704.2	NP_001166175.1
Q9NZ52-4	NM_001172703.2	NP_001166174.1
Q9NZ52-4	NM_001291641.1	NP_001278570.1

Amino acid sequences of our canonical and alternatively spliced GGA3

accession_id	Protein sequence
Q9NZ52-1	MAEAEGESLESWLNKATNPSNRQEDWEYIIGFCDQINKELEGPQIAVRLLAHKIQSPQEWEALQALTVLEACMKNCGRRFHNEVGKFRFL NELIKVVSPKYLGDRVSEKVKTKVIELLYSWTMALPEEAKIKDAYHMLKRQGIVQSDPPIPVDRTLIPSPPPRPKNPVFDDEEKSKLLAK LLKSKNPDDLQEANKLIKSMVKEDEARIQKVTKRLHTLEEVNNNVRLLSEMLLHYSQEDSSDGDRELMKELFDQCENKRRTLFKLASETE DNDNSLGDILQASDNLSRVINSYKTIIEGQVINGEVATLTLPDSEGNSQCSNQGTLIDLAELDTTNSLSSVLAPAPTPPSSGIPILPPPP QASGPPRSRSSSQAEATLGPSSTSNALSWLDEELLCLGLADPAPNVPPKESAGNSQWHLLQREQSDLDFFSPRPGTAACGASDAPLLQPS APSSSSSQAPLPPPFPAPVVPASVPAPSAGSSLFSTGVAPALAPKVEPAVPGHHGLALGNSALHHLDALDQLLEEAKVTSGLVKPTTSPL IPTTTPARPLLPFSTGPGSPLFQPLSFQSQGSPPKGPELSLASIHVPLESIKPSSALPVTAYDKNGFRILFHFAKECPPGRPDVLVVVVS MLNTAPLPVKSIVLQAAVPKSMKVKLQPPSGTELSPFSPIQPPAAITQVMLLANPLKEKVRLRYKLTFALGEQLSTEVGEVDQFPPVEQW
Q9NZ52-2	MAEAEGESLESWLNKATNPSNRQEDWEYIIGFCDQINKELEGPQIAVRLLAHKIQSPQEWEALQALTYLGDRVSEKVKTKVIELLYSWTM ALPEEAKIKDAYHMLKRQGIVQSDPPIPVDRTLIPSPPPRPKNPVFDDEEKSKLLAKLLKSKNPDDLQEANKLIKSMVKEDEARIQKVTK RLHTLEEVNNNVRLLSEMLLHYSQEDSSDGDRELMKELFDQCENKRRTLFKLASETEDNDNSLGDILQASDNLSRVINSYKTIIEGQVIN GEVATLTLPDSEGNSQCSNQGTLIDLAELDTTNSLSSVLAPAPTPPSSGIPILPPPPQASGPPRSRSSSQAEATLGPSSTSNALSWLDEE LLCLGLADPAPNVPPKESAGNSQWHLLQREQSDLDFFSPRPGTAACGASDAPLLQPSAPSSSSSQAPLPPPFPAPVVPASVPAPSAGSSL FSTGVAPALAPKVEPAVPGHHGLALGNSALHHLDALDQLLEEAKVTSGLVKPTTSPLIPTTTPARPLLPFSTGPGSPLFQPLSFQSQGSP PKGPELSLASIHVPLESIKPSSALPVTAYDKNGFRILFHFAKECPPGRPDVLVVVVSMLNTAPLPVKSIVLQAAVPKSMKVKLQPPSGTE
Q9NZ52-3	MALPEEAKIKDAYHMLKRQGIVQSDPPIPVDRTLIPSPPPRPKNPVFDDEEKSKLLAKLLKSKNPDDLQEANKLIKSMVKEDEARIQKVT KRLHTLEEVNNNVRLLSEMLLHYSQEDSSDGDRELMKELFDQCENKRRTLFKLASETEDNDNSLGDILQASDNLSRVINSYKTIIEGQVI NGEVATLTLPDSEGNSQCSNQGTLIDLAELDTTNSLSSVLAPAPTPPSSGIPILPPPPQASGPPRSRSSSQAEATLGPSSTSNALSWLDE ELLCLGLADPAPNVPPKESAGNSQWHLLQREQSDLDFFSPRPGTAACGASDAPLLQPSAPSSSSSQAPLPPPFPAPVVPASVPAPSAGSS LFSTGVAPALAPKVEPAVPGHHGLALGNSALHHLDALDQLLEEAKVTSGLVKPTTSPLIPTTTPARPLLPFSTGPGSPLFQPLSFQSQGS PPKGPELSLASIHVPLESIKPSSALPVTAYDKNGFRILFHFAKECPPGRPDVLVVVVSMLNTAPLPVKSIVLQAAVPKSMKVKLQPPSGT
Q9NZ52-4	MKNCGRRFHNEVGKFRFLNELIKVVSPKYLGDRVSEKVKTKVIELLYSWTMALPEEAKIKDAYHMLKRQGIVQSDPPIPVDRTLIPSPPP RPKNPVFDDEEKSKLLAKLLKSKNPDDLQEANKLIKSMVKEDEARIQKVTKRLHTLEEVNNNVRLLSEMLLHYSQEDSSDGDRELMKELF DQCENKRRTLFKLASETEDNDNSLGDILQASDNLSRVINSYKTIIEGQVINGEVATLTLPDSEGNSQCSNQGTLIDLAELDTTNSLSSVL APAPTPPSSGIPILPPPPQASGPPRSRSSSQAEATLGPSSTSNALSWLDEELLCLGLADPAPNVPPKESAGNSQWHLLQREQSDLDFFSP RPGTAACGASDAPLLQPSAPSSSSSQAPLPPPFPAPVVPASVPAPSAGSSLFSTGVAPALAPKVEPAVPGHHGLALGNSALHHLDALDQL LEEAKVTSGLVKPTTSPLIPTTTPARPLLPFSTGPGSPLFQPLSFQSQGSPPKGPELSLASIHVPLESIKPSSALPVTAYDKNGFRILFH FAKECPPGRPDVLVVVVSMLNTAPLPVKSIVLQAAVPKSMKVKLQPPSGTELSPFSPIQPPAAITQVMLLANPLKEKVRLRYKLTFALGE

Protein Functional Features

Main function of this protein. (from UniProt)

GGA3 (go to UniProt):Q9NZ52

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
Q9NZ52	Domain	16	146	Note=VHS;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00218	Type=Deletion;Start=68;End=100
Q9NZ52	Domain	16	146	Note=VHS;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00218	Type=Deletion;Start=1;End=122
Q9NZ52	Domain	16	146	Note=VHS;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00218	Type=Deletion;Start=1;End=72
Q9NZ52	Domain	594	715	Note=GAE;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00093	Type=Substitution;Start=688;End=723
Q9NZ52	Region	1	313	Note=Binds to ARF1 (in long isoform)	Type=Deletion;Start=68;End=100
Q9NZ52	Region	1	313	Note=Binds to ARF1 (in long isoform)	Type=Deletion;Start=1;End=122
Q9NZ52	Region	1	313	Note=Binds to ARF1 (in long isoform)	Type=Deletion;Start=1;End=72

Gene Isoform Structures and Expression Levels for GGA3

Gene structures of our canonical and alternative spliced genes of GGA3
* 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 Q9NZ52-1

3D view using mol* of Q9NZ52-2

3D view using mol* of Q9NZ52-3

3D view using mol* of Q9NZ52-4

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 Q9NZ52-1

pLDDT distribution across the protein length of Q9NZ52-2

pLDDT distribution across the protein length of Q9NZ52-3

pLDDT distribution across the protein length of Q9NZ52-4

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 Q9NZ52-1

Ramachandran plot of Q9NZ52-3

Ramachandran plot of Q9NZ52-4

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
Q9NZ52-1	1.005	91	1.096	289.149	0.695	0.598	0.747	1.256	0.49	2.563	2.144	166,168,169,178,197,198,200,201,202,204,205,208,20 9,212,213,635,636,637,666,667,668,669,670,700
Q9NZ52-2	1.014	74	1.041	195.853	0.431	0.783	1.009	2.211	0.729	3.035	0.4	66,68,69,70,71,72,73,77,78,81,82,85,105,110,111
Q9NZ52-3	0.732	50	0.685	135.142	0.606	0.619	0.857	0.313	1.076	0.291	0.229	1,2,3,4,9,10,13,14,25,26,28
Q9NZ52-4	0.891	66	0.796	126.224	0.476	0.74	0.995	0.545	1.262	0.432	0.631	1,2,9,41,44,45,48,49,52,53,78,79,82,83,85

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 Q9NZ52-1_Q9NZ52-1_1lf8_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 Q9NZ52-1_1lf8_B_Q9NZ52-2.pdb

3D view using mol* of Q9NZ52-1_1lf8_B_Q9NZ52-3.pdb

3D view using mol* of Q9NZ52-1_1lf8_B_Q9NZ52-4.pdb

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

3D view using mol* of Q9NZ52-1_Q9NZ52-2.pdb

3D view using mol* of Q9NZ52-1_Q9NZ52-3.pdb

3D view using mol* of Q9NZ52-1_Q9NZ52-4.pdb

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

./stats/secondary_structure/figure/Q9NZ52-1_vs_Q9NZ52-2.png

./stats/secondary_structure/figure/Q9NZ52-1_vs_Q9NZ52-3.png

./stats/secondary_structure/figure/Q9NZ52-1_vs_Q9NZ52-4.png

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

./stats/relative_asa/Q9NZ52-1_vs_Q9NZ52-2.png

./stats/relative_asa/Q9NZ52-1_vs_Q9NZ52-3.png

./stats/relative_asa/Q9NZ52-1_vs_Q9NZ52-4.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 GGA3

Drugs targeting this gene/protein.
(DrugBank)

UniProt accession

Gene name

DrugBank ID

Drug name

Drug group

Actions

Related Diseases to GGA3

Previous studies relating to the alternative splicing of GGA3 and disease information from the MeSH term (PubMed)

Gene

PMID

Title

Abstract

MeSH ID

MeSH term

Clinically important variants in GGA3

(ClinVar, 04/20/2024)

accession_id

uniprot_id

gene_name

Type

Variant

Clinical_significance