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UniProtKB - P0DTC3 (AP3A_SARS2)

Entry version 11 (25 May 2022)
Sequence version 1 (22 Apr 2020)
Previous versions | rss
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Protein

ORF3a protein

Gene

3a

Organism
Severe acute respiratory syndrome coronavirus 2 (2019-nCoV) (SARS-CoV-2)
Status
Reviewed-Annotation score:

Annotation score:5 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the 'correct annotation' for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the 'protein existence' evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

Plays a role in viral egress via lysosomal trafficking (PubMed:33157038, PubMed:33422265).

Forms homotetrameric ion channels (viroporin) localized at endosomes and lysosomes, that may induce deacidification of lysosomes, allowing safe egress of virions via lysosomal trafficking (PubMed:33157038, PubMed:33422265,PubMed:34158638).

Also blocks autolysosomes formation by binding and sequestering the host component VPS39 for homotypic fusion and protein sorting (HOPS) on late endosomes. This prevents fusion of autophagosomes with lysosomes, disrupting autophagy and facilitating virus egress (PubMed:33422265).

3 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection describes interesting single amino acid sites on the sequence that are not defined in any other subsection. This subsection can be displayed in different sections ('Function', 'PTM / Processing', 'Pathology and Biotech') according to its content.<p><a href='/help/site' target='_top'>More...</a></p>Sitei133Involved in polymerizationBy similarity1

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

Complete GO annotation on QuickGO ...

GO - Biological processi

Complete GO annotation on QuickGO ...

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionIon channel, Viral ion channel
Biological processIon transport, Transport

Enzyme and pathway databases

Reactome - a knowledgebase of biological pathways and processes

More...Reactomei		R-HSA-9694322, Virion Assembly and Release
R-HSA-9694614, Attachment and Entry
R-HSA-9694635, Translation of Structural Proteins
R-HSA-9694719, Maturation of protein 3a

Protein family/group databases

Transport Classification Database

More...TCDBi		1.A.57.1.5, the human sars coronavirus viroporin (sars-vp)

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
ORF3a protein
Short name:
ORF3a
Alternative name(s):
Accessory protein 3a
Protein 3a
Protein U274
Protein X1
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: 'Name', 'Synonyms', 'Ordered locus names' and 'ORF names'.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
ORF Names:3a
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiSevere acute respiratory syndrome coronavirus 2 (2019-nCoV) (SARS-CoV-2)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the 'taxonomic identifier' or 'taxid'.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri2697049 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiViruses › Riboviria › Orthornavirae › Pisuviricota › Pisoniviricetes › Nidovirales › Cornidovirineae › Coronaviridae › Orthocoronavirinae › Betacoronavirus › Sarbecovirus ›
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section only exists in viral entries and indicates the host(s) either as a specific organism or taxonomic group of organisms that are susceptible to be infected by a virus.<p><a href='/help/virus_host' target='_top'>More...</a></p>Virus hostiHomo sapiens (Human) [TaxID: 9606]
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000464024 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">proteome</a> can consist of several components.<br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Genome

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/subcellular%5Flocation%5Fsection">'Subcellular location'</a> section describes the subcellular compartment where each non-membrane region of a membrane-spanning protein is found.<p><a href='/help/topo_dom' target='_top'>More...</a></p>Topological domaini1 – 42Extracellular1 PublicationAdd BLAST42
<p>This subsection of the <a href="http://www.uniprot.org/help/subcellular%5Flocation%5Fsection">'Subcellular location'</a> section describes the extent of a membrane-spanning region of the protein. It denotes the presence of both alpha-helical transmembrane regions and the membrane spanning regions of beta-barrel transmembrane proteins.<p><a href='/help/transmem' target='_top'>More...</a></p>Transmembranei43 – 61Helical1 PublicationAdd BLAST19
Topological domaini62 – 67Cytoplasmic1 Publication6
Transmembranei68 – 93Helical1 PublicationAdd BLAST26
Topological domaini94 – 101Extracellular1 Publication8
Transmembranei102 – 126Helical1 PublicationAdd BLAST25
Topological domaini127 – 275Cytoplasmic1 PublicationAdd BLAST149

Keywords - Cellular componenti

Host cell membrane, Host cytoplasm, Host endosome, Host lysosome, Host membrane, Membrane, Secreted, Virion

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/manual/pathology%5Fand%5Fbiotech%5Fsection">'Pathology and Biotech'</a> section describes the effect of the experimental mutation of one or more amino acid(s) on the biological properties of the protein.<p><a href='/help/mutagen' target='_top'>More...</a></p>Mutagenesisi1 – 41Missing : Partial loss of Ca(2+) and NMDG(+) permeability. Increased localization at host plasma membrane. 1 PublicationAdd BLAST41
Mutagenesisi57 – 58QS → EL: Partial loss of Ca(2+) and NMDG(+) permeability. 1 Publication2
Mutagenesisi57Q → H: No effect on ion permeability. 1 Publication1
Mutagenesisi116Q → L: Partial loss of Ca(2+) and NMDG(+) permeability. 1 Publication1

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'PTM / Processing' section describes the extent of a polypeptide chain in the mature protein following processing or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00004496501 – 275ORF3a proteinAdd BLAST275

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/ptm%5Fprocessing%5Fsection">PTM / Processing</a> section specifies the position and type of each covalently attached glycan group (mono-, di-, or polysaccharide).<p><a href='/help/carbohyd' target='_top'>More...</a></p>Glycosylationi32O-linked (GalNAc...) threonine; by hostBy similarity1
Glycosylationi34O-linked (GalNAc...) threonine; by hostSequence analysis1

<p>This subsection of the <a href="http://www.uniprot.org/help/ptm%5Fprocessing%5Fsection">PTM/processing</a> section describes post-translational modifications (PTMs). This subsection <strong>complements</strong> the information provided at the sequence level or describes modifications for which <strong>position-specific data is not yet available</strong>.<p><a href='/help/post-translational_modification' target='_top'>More...</a></p>Post-translational modificationi

Exists in both O-glycosylated and non-glycosylated forms. The glycosylated form is associated with the virion.By similarity

Keywords - PTMi

Glycoprotein

PTM databases

GlyGen: Computational and Informatics Resources for Glycoscience

More...GlyGeni		P0DTC3, 2 sites

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction%5Fsection">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function%5Fsection">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Homodimer (PubMed:34158638), a subset forms homotetramer of two homodimers linked non covalently (PubMed:34158638, PubMed:34158638).

Interacts with M, S and E proteins.

Also interacts with the accessory protein 7a (By similarity).

Interacts with host VPS39, sequestering it on late endosomes (PubMed:33422265).

By similarity2 Publications

<p>This subsection of the '<a href="http://www.uniprot.org/help/interaction%5Fsection">Interaction</a>' section provides information about binary protein-protein interactions. The data presented in this section are a quality-filtered subset of binary interactions automatically derived from the <a href="https://www.ebi.ac.uk/intact/">IntAct database</a>. It is updated at every <a href="http://www.uniprot.org/help/synchronization">UniProt release</a>.<p><a href='/help/binary_interactions' target='_top'>More...</a></p>Binary interactionsi

Hide details

GO - Molecular functioni

Complete GO annotation on QuickGO ...

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGRID)

More...BioGRIDi		4383868, 1111 interactors

ComplexPortal: manually curated resource of macromolecular complexes

More...ComplexPortali		CPX-6098, SARS-CoV-2 3a complex

Protein interaction database and analysis system

More...IntActi		P0DTC3, 442 interactors

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

Secondary structure

1275
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

More...SMRi		P0DTC3

Database of comparative protein structure models

More...ModBasei		Search...

Protein Data Bank in Europe - Knowledge Base

More...PDBe-KBi		Search...

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/family%5Fand%5Fdomains%5Fsection">Family and Domains</a> section describes the position and type of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.<p><a href='/help/domain' target='_top'>More...</a></p>Domaini33 – 141CoV 3a-like viroporin TMPROSITE-ProRule annotationAdd BLAST109
Domaini145 – 237CoV 3a-like viroporin CDPROSITE-ProRule annotationAdd BLAST93

<p>This subsection of the 'Family and domains' section provides general information on the biological role of a domain. The term 'domain' is intended here in its wide acceptation, it may be a structural domain, a transmembrane region or a functional domain. Several domains are described in this subsection.<p><a href='/help/domain_cc' target='_top'>More...</a></p>Domaini

The second or the third transmembrane region are responsible for Golgi localization.By similarity

Keywords - Domaini

Transmembrane, Transmembrane helix

Family and domain databases

Conserved Domains Database

More...CDDi		cd21648, SARS-CoV-like_ORF3a, 1 hit

Database of protein disorder

More...DisProti		DP03003

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR024407, Protein_3a_bCoV

Pfam protein domain database

More...Pfami		View protein in Pfam
PF11289, bCoV_viroporin, 1 hit

PROSITE; a protein domain and family database

More...PROSITEi		View protein in PROSITE
PS51967, COV_VIROPORIN_3A_CD, 1 hit
PS51966, COV_VIROPORIN_3A_TM, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence%5Flength">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

P0DTC3-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MDLFMRIFTI GTVTLKQGEI KDATPSDFVR ATATIPIQAS LPFGWLIVGV 
        60         70         80         90        100
ALLAVFQSAS KIITLKKRWQ LALSKGVHFV CNLLLLFVTV YSHLLLVAAG 
       110        120        130        140        150
LEAPFLYLYA LVYFLQSINF VRIIMRLWLC WKCRSKNPLL YDANYFLCWH 
       160        170        180        190        200
TNCYDYCIPY NSVTSSIVIT SGDGTTSPIS EHDYQIGGYT EKWESGVKDC 
       210        220        230        240        250
VVLHSYFTSD YYQLYSTQLS TDTGVEHVTF FIYNKIVDEP EEHVQIHTID 
       260        270 
GSSGVVNPVM EPIYDEPTTT TSVPL
Length:275
Mass (Da):31,123
Last modified:April 22, 2020 - v1
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i4688E6D477E031C4
GO

<p>This subsection of the 'Sequence' section provides information on polymorphic variants. If the variant is associated with a disease state, the description of the latter can be found in the <a href="http://www.uniprot.org/manual/involvement%5Fin%5Fdisease">'Involvement in disease'</a> subsection.<p><a href='/help/polymorphism' target='_top'>More...</a></p>Polymorphismi

Variant Omicron/BA.1 and BA.2 belong to a lineage first isolated in South Africa (November 2021).Curated

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Sequence' section describes natural variant(s) of the protein sequence.<p><a href='/help/variant' target='_top'>More...</a></p>Natural varianti26S → L in strain: Delta/B.1.617.2 and Kappa/B.1.617.1. Curated1
Natural varianti42P → L in strain: Iota/B.1.526. Curated1
Natural varianti57Q → H in strain: Beta/B.1.351, Epsilon/B.1.429, Iota/B.1.526 and Mu/B.1621. Curated1
Natural varianti171S → L in strain: Beta/B.1.351. Curated1
Natural varianti223T → I in strain: Omicron/BA.2. 1
Natural varianti253S → P in strain: Gamma/P.1. Curated1
Natural varianti257Missing in strain: Mu/B.1.621. Curated1

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...EMBLi

GenBank nucleotide sequence database

More...GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...DDBJi
Links Updated
MN908947 Genomic RNA Translation: QHD43417.1

NCBI Reference Sequences

More...RefSeqi		YP_009724391.1, NC_045512.2

Genome annotation databases

Database of genes from NCBI RefSeq genomes

More...GeneIDi		43740569

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		vg:43740569

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
MN908947 Genomic RNA Translation: QHD43417.1
RefSeqiYP_009724391.1, NC_045512.2

3D structure databases

Select the link destinations:

Protein Data Bank Europe

More...PDBei

Protein Data Bank RCSB

More...RCSB PDBi

Protein Data Bank Japan

More...PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
6XDCelectron microscopy2.90A/B1-275[»]
7KJRelectron microscopy2.08A/B1-275[»]
SMRiP0DTC3
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

BioGRIDi4383868, 1111 interactors
ComplexPortaliCPX-6098, SARS-CoV-2 3a complex
IntActiP0DTC3, 442 interactors

Protein family/group databases

TCDBi1.A.57.1.5, the human sars coronavirus viroporin (sars-vp)

PTM databases

GlyGeniP0DTC3, 2 sites

Protocols and materials databases

The DNASU plasmid repository

More...DNASUi		43740569

Genome annotation databases

GeneIDi43740569
KEGGivg:43740569

Enzyme and pathway databases

ReactomeiR-HSA-9694322, Virion Assembly and Release
R-HSA-9694614, Attachment and Entry
R-HSA-9694635, Translation of Structural Proteins
R-HSA-9694719, Maturation of protein 3a

Miscellaneous databases

Protein Ontology

More...PROi		PR:P0DTC3

Family and domain databases

CDDicd21648, SARS-CoV-like_ORF3a, 1 hit
DisProtiDP03003
InterProiView protein in InterPro
IPR024407, Protein_3a_bCoV
PfamiView protein in Pfam
PF11289, bCoV_viroporin, 1 hit
PROSITEiView protein in PROSITE
PS51967, COV_VIROPORIN_3A_CD, 1 hit
PS51966, COV_VIROPORIN_3A_TM, 1 hit

MobiDB: a database of protein disorder and mobility annotations

More...MobiDBi		Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the 'Entry information' section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiAP3A_SARS2
<p>This subsection of the 'Entry information' section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called 'Primary (citable) accession number'.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: P0DTC3
<p>This subsection of the 'Entry information' section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification ('Last modified'). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: April 22, 2020
Last sequence update: April 22, 2020
Last modified: May 25, 2022
This is version 11 of the entry and version 1 of the sequence. See complete history.
<p>This subsection of the 'Entry information' section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

<p>This section contains any relevant information that doesn't fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

3D-structure, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
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