ID AP3A_SARS2 Reviewed; 275 AA. AC P0DTC3; DT 22-APR-2020, integrated into UniProtKB/Swiss-Prot. DT 22-APR-2020, sequence version 1. DT 27-MAR-2024, entry version 20. DE RecName: Full=ORF3a protein; DE Short=ORF3a; DE AltName: Full=Accessory protein 3a; DE AltName: Full=Protein 3a; DE AltName: Full=Protein U274; DE AltName: Full=Protein X1; GN ORFNames=3a; OS Severe acute respiratory syndrome coronavirus 2 (2019-nCoV) (SARS-CoV-2). OC Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; OC Nidovirales; Cornidovirineae; Coronaviridae; Orthocoronavirinae; OC Betacoronavirus; Sarbecovirus; OC Severe acute respiratory syndrome coronavirus. OX NCBI_TaxID=2697049; OH NCBI_TaxID=9606; Homo sapiens (Human). RN [1] RP NUCLEOTIDE SEQUENCE [GENOMIC RNA]. RX PubMed=32015508; DOI=10.1038/s41586-020-2008-3; RA Wu F., Zhao S., Yu B., Chen Y.-M., Wang W., Song Z.-G., Hu Y., Tao Z.-W., RA Tian J.-H., Pei Y.-Y., Yuan M.-L., Zhang Y.-L., Dai F.-H., Liu Y., RA Wang Q.-M., Zheng J.-J., Xu L., Holmes E.C., Zhang Y.-Z.; RT "A new coronavirus associated with human respiratory disease in China."; RL Nature 579:265-269(2020). RN [2] RP SUBCELLULAR LOCATION. RX PubMed=33060197; DOI=10.1126/science.abe9403; RG QCRG Structural Biology Consortium; RG Zoonomia Consortium; RA Gordon D.E., Hiatt J., Bouhaddou M., Rezelj V.V., Ulferts S., Braberg H., RA Jureka A.S., Obernier K., Guo J.Z., Batra J., Kaake R.M., Weckstein A.R., RA Owens T.W., Gupta M., Pourmal S., Titus E.W., Cakir M., Soucheray M., RA McGregor M., Cakir Z., Jang G., O'Meara M.J., Tummino T.A., Zhang Z., RA Foussard H., Rojc A., Zhou Y., Kuchenov D., Huettenhain R., Xu J., RA Eckhardt M., Swaney D.L., Fabius J.M., Ummadi M., Tutuncuoglu B., RA Rathore U., Modak M., Haas P., Haas K.M., Naing Z.Z.C., Pulido E.H., RA Shi Y., Barrio-Hernandez I., Memon D., Petsalaki E., Dunham A., RA Marrero M.C., Burke D., Koh C., Vallet T., Silvas J.A., Azumaya C.M., RA Billesboelle C., Brilot A.F., Campbell M.G., Diallo A., Dickinson M.S., RA Diwanji D., Herrera N., Hoppe N., Kratochvil H.T., Liu Y., Merz G.E., RA Moritz M., Nguyen H.C., Nowotny C., Puchades C., Rizo A.N., RA Schulze-Gahmen U., Smith A.M., Sun M., Young I.D., Zhao J., Asarnow D., RA Biel J., Bowen A., Braxton J.R., Chen J., Chio C.M., Chio U.S., RA Deshpande I., Doan L., Faust B., Flores S., Jin M., Kim K., Lam V.L., RA Li F., Li J., Li Y.L., Li Y., Liu X., Lo M., Lopez K.E., Melo A.A., RA Moss F.R. III, Nguyen P., Paulino J., Pawar K.I., Peters J.K., RA Pospiech T.H. Jr., Safari M., Sangwan S., Schaefer K., Thomas P.V., RA Thwin A.C., Trenker R., Tse E., Tsui T.K.M., Wang F., Whitis N., Yu Z., RA Zhang K., Zhang Y., Zhou F., Saltzberg D., Hodder A.J., Shun-Shion A.S., RA Williams D.M., White K.M., Rosales R., Kehrer T., Miorin L., Moreno E., RA Patel A.H., Rihn S., Khalid M.M., Vallejo-Gracia A., Fozouni P., RA Simoneau C.R., Roth T.L., Wu D., Karim M.A., Ghoussaini M., Dunham I., RA Berardi F., Weigang S., Chazal M., Park J., Logue J., McGrath M., RA Weston S., Haupt R., Hastie C.J., Elliott M., Brown F., Burness K.A., RA Reid E., Dorward M., Johnson C., Wilkinson S.G., Geyer A., Giesel D.M., RA Baillie C., Raggett S., Leech H., Toth R., Goodman N., Keough K.C., RA Lind A.L., Klesh R.J., Hemphill K.R., Carlson-Stevermer J., Oki J., RA Holden K., Maures T., Pollard K.S., Sali A., Agard D.A., Cheng Y., RA Fraser J.S., Frost A., Jura N., Kortemme T., Manglik A., Southworth D.R., RA Stroud R.M., Alessi D.R., Davies P., Frieman M.B., Ideker T., Abate C., RA Jouvenet N., Kochs G., Shoichet B., Ott M., Palmarini M., Shokat K.M., RA Garcia-Sastre A., Rassen J.A., Grosse R., Rosenberg O.S., Verba K.A., RA Basler C.F., Vignuzzi M., Peden A.A., Beltrao P., Krogan N.J.; RT "Comparative host-coronavirus protein interaction networks reveal pan-viral RT disease mechanisms."; RL Science 0:0-0(2020). RN [3] RP FUNCTION. RX PubMed=33157038; DOI=10.1016/j.cell.2020.10.039; RA Ghosh S., Dellibovi-Ragheb T.A., Kerviel A., Pak E., Qiu Q., Fisher M., RA Takvorian P.M., Bleck C., Hsu V.W., Fehr A.R., Perlman S., Achar S.R., RA Straus M.R., Whittaker G.R., de Haan C.A.M., Kehrl J., Altan-Bonnet G., RA Altan-Bonnet N.; RT "beta-Coronaviruses Use Lysosomes for Egress Instead of the Biosynthetic RT Secretory Pathway."; RL Cell 183:1520-1535(2020). RN [4] RP FUNCTION, INTERACTION WITH HOST VPS39, AND SUBCELLULAR LOCATION. RX PubMed=33422265; DOI=10.1016/j.devcel.2020.12.010; RA Miao G., Zhao H., Li Y., Ji M., Chen Y., Shi Y., Bi Y., Wang P., Zhang H.; RT "ORF3a of the COVID-19 virus SARS-CoV-2 blocks HOPS complex-mediated RT assembly of the SNARE complex required for autolysosome formation."; RL Dev. Cell 56:427-442(2020). RN [5] RP FUNCTION, INTERACTION WITH HOST HMGB1 AND HOST HMOX1, AND SUBCELLULAR RP LOCATION. RX PubMed=35239449; DOI=10.1080/15548627.2022.2039992; RA Zhang X., Yang Z., Pan T., Long X., Sun Q., Wang P.H., Li X., Kuang E.; RT "SARS-CoV-2 ORF3a induces RETREG1/FAM134B-dependent reticulophagy and RT triggers sequential ER stress and inflammatory responses during SARS-CoV-2 RT infection."; RL Autophagy 0:0-0(2022). RN [6] RP DISORDERED REGIONS. RX PubMed=35108439; DOI=10.1111/febs.16379; RA Quaglia F., Salladini E., Carraro M., Minervini G., Tosatto S.C.E., RA Le Mercier P.; RT "SARS-CoV-2 variants preferentially emerge at intrinsically disordered RT protein sites helping immune evasion."; RL FEBS J. 289:4240-4250(2022). RN [7] RP STRUCTURE BY ELECTRON MICROSCOPY (2.1 ANGSTROMS), FUNCTION, SUBUNIT, RP MUTAGENESIS OF 1-MET--LEU-41; 57-GLN-SER-58; GLN-57 AND GLN-116, AND RP SUBCELLULAR LOCATION. RX PubMed=34158638; DOI=10.1038/s41594-021-00619-0; RA Kern D.M., Sorum B., Mali S.S., Hoel C.M., Sridharan S., Remis J.P., RA Toso D.B., Kotecha A., Bautista D.M., Brohawn S.G.; RT "Cryo-EM structure of SARS-CoV-2 ORF3a in lipid nanodiscs."; RL Nat. Struct. Mol. Biol. 28:573-582(2021). CC -!- FUNCTION: Plays a role in viral egress via lysosomal trafficking CC (PubMed:33157038, PubMed:33422265). Forms homotetrameric ion channels CC (viroporins) localized at endosomes and lysosomes, that may induce CC deacidification of lysosomes, allowing safe egress of virions via CC lysosomal trafficking (PubMed:33157038, PubMed:33422265, CC PubMed:34158638). Also blocks autolysosome formation by binding and CC sequestering the host component VPS39 for homotypic fusion and protein CC sorting (HOPS) on late endosomes (PubMed:33422265). This prevents CC fusion of autophagosomes with lysosomes, disrupting autophagy and CC facilitating virus egress (PubMed:33422265). Induces host CC RETREG1/FAM134B-dependent reticulophagy by interacting with host HMGB1 CC and enhancing the association between HMGB1 and host BECN1 CC (PubMed:35239449). This induces endoplasmic reticulum stress and CC inflammatory responses and facilitates viral infection CC (PubMed:35239449). {ECO:0000269|PubMed:33157038, CC ECO:0000269|PubMed:33422265, ECO:0000269|PubMed:34158638, CC ECO:0000269|PubMed:35239449}. CC -!- SUBUNIT: Homodimer (PubMed:34158638), a subset forms homotetramer of CC two homodimers linked non covalently (PubMed:34158638, CC PubMed:34158638). Interacts with M, S and E proteins. Also interacts CC with the accessory protein 7a (By similarity). Interacts with host CC VPS39, sequestering it on late endosomes (PubMed:33422265). Interacts CC with host HMGB1; the interaction enhances the association between HMGB1 CC and host BECN1, promoting reticulophagy (PubMed:35239449). Interacts CC with HMOX1; the interaction promotes ORF3A-induced autophagy but is CC unlikely to be involved in ORF3A-mediated induction of reticulophagy CC (PubMed:35239449). {ECO:0000250|UniProtKB:P59632, CC ECO:0000269|PubMed:33422265, ECO:0000269|PubMed:34158638, CC ECO:0000269|PubMed:35239449}. CC -!- INTERACTION: CC P0DTC3; P0DTC3: 3a; NbExp=2; IntAct=EBI-25475894, EBI-25475894; CC P0DTC3; Q9Y673: ALG5; Xeno; NbExp=4; IntAct=EBI-25475894, EBI-11725055; CC P0DTC3; Q01518: CAP1; Xeno; NbExp=3; IntAct=EBI-25475894, EBI-2808398; CC P0DTC3; P09601: HMOX1; Xeno; NbExp=4; IntAct=EBI-25475894, EBI-2806151; CC P0DTC3; Q12846: STX4; Xeno; NbExp=4; IntAct=EBI-25475894, EBI-744942; CC P0DTC3; Q8NBJ7: SUMF2; Xeno; NbExp=3; IntAct=EBI-25475894, EBI-723091; CC P0DTC3; Q9UH99: SUN2; Xeno; NbExp=3; IntAct=EBI-25475894, EBI-1044964; CC P0DTC3; Q9P2Y5: UVRAG; Xeno; NbExp=6; IntAct=EBI-25475894, EBI-2952704; CC P0DTC3; P51809: VAMP7; Xeno; NbExp=4; IntAct=EBI-25475894, EBI-1052205; CC P0DTC3; Q96JC1: VPS39; Xeno; NbExp=19; IntAct=EBI-25475894, EBI-1050197; CC P0DTC3; P49754: VPS41; Xeno; NbExp=4; IntAct=EBI-25475894, EBI-2130459; CC P0DTC3; Q8NAF0: ZNF579; Xeno; NbExp=2; IntAct=EBI-25475894, EBI-6164383; CC -!- SUBCELLULAR LOCATION: Virion {ECO:0000250|UniProtKB:P59632}. Host cell CC membrane {ECO:0000250|UniProtKB:P59632, ECO:0000269|PubMed:33060197, CC ECO:0000269|PubMed:34158638}; Multi-pass membrane protein CC {ECO:0000250|UniProtKB:P59632, ECO:0000269|PubMed:34158638}. Host CC endoplasmic reticulum membrane {ECO:0000269|PubMed:35239449}; Multi- CC pass membrane protein {ECO:0000269|PubMed:34158638}. Secreted CC {ECO:0000250|UniProtKB:P59632}. Host cytoplasm CC {ECO:0000250|UniProtKB:P59632, ECO:0000269|PubMed:33060197}. Host CC endosome {ECO:0000269|PubMed:33060197, ECO:0000269|PubMed:33422265}. CC Host lysosome {ECO:0000269|PubMed:33422265}. Note=The cell surface CC expressed protein can undergo endocytosis. The protein is secreted in CC association with membranous structures. {ECO:0000250|UniProtKB:P59632}. CC -!- DOMAIN: The second or the third transmembrane region are responsible CC for Golgi localization. {ECO:0000250|UniProtKB:P59632}. CC -!- PTM: Exists in both O-glycosylated and non-glycosylated forms. The CC glycosylated form is associated with the virion. CC {ECO:0000250|UniProtKB:P59632}. CC -!- POLYMORPHISM: Variant Omicron/BA.1 and BA.2 belong to a lineage first CC isolated in South Africa (November 2021). {ECO:0000305}. CC -!- POLYMORPHISM: Variant Omicron/BQ.1.1 belongs to a lineage first CC isolated in Nigeria (November 2022). {ECO:0000305}. CC -!- POLYMORPHISM: Variant Omicron/XBB.1.5 belongs to a lineage first CC isolated in United States (November 2022). It is the result of CC recombination between omicron BJ.1 and BM.1.1. Moreover XBB.1.5 do not CC express ORF8. {ECO:0000305}. CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- DR EMBL; MN908947; QHD43417.1; -; Genomic_RNA. DR PDB; 6XDC; EM; 2.90 A; A/B=1-275. DR PDB; 7KJR; EM; 2.08 A; A/B=1-275. DR PDB; 8EQJ; EM; 3.00 A; A/B=1-275. DR PDB; 8EQT; EM; 3.40 A; A/B=1-275. DR PDB; 8EQU; EM; 2.80 A; A/B=1-275. DR PDB; 8T5P; X-ray; 2.50 A; G/H/I=36-40. DR PDB; 8T5Q; X-ray; 1.90 A; G/H/I=36-40. DR PDBsum; 6XDC; -. DR PDBsum; 7KJR; -. DR PDBsum; 8EQJ; -. DR PDBsum; 8EQT; -. DR PDBsum; 8EQU; -. DR PDBsum; 8T5P; -. DR PDBsum; 8T5Q; -. DR EMDB; EMD-22136; -. DR EMDB; EMD-22898; -. DR SMR; P0DTC3; -. DR BioGRID; 4383868; 1250. DR ComplexPortal; CPX-6098; SARS-CoV-2 3a complex. DR IntAct; P0DTC3; 466. DR MINT; P0DTC3; -. DR TCDB; 1.A.57.1.5; the human sars coronavirus viroporin (sars-vp) family. DR GlyGen; P0DTC3; 2 sites. DR iPTMnet; P0DTC3; -. DR DNASU; 43740569; -. DR AGR; RefSeq:YP_009724391; -. DR Reactome; R-HSA-9694322; Virion Assembly and Release. DR Reactome; R-HSA-9694614; Attachment and Entry. DR Reactome; R-HSA-9694635; Translation of Structural Proteins. DR Reactome; R-HSA-9694719; Maturation of protein 3a. DR Reactome; R-HSA-9705671; SARS-CoV-2 activates/modulates innate and adaptive immune responses. DR Reactome; R-HSA-9733458; Induction of Cell-Cell Fusion. DR Reactome; R-HSA-9754560; SARS-CoV-2 modulates autophagy. DR Reactome; R-HSA-9755779; SARS-CoV-2 targets host intracellular signalling and regulatory pathways. DR PRO; PR:P0DTC3; -. DR Proteomes; UP000464024; Genome. DR GO; GO:0005576; C:extracellular region; IEA:UniProtKB-SubCell. DR GO; GO:0044165; C:host cell endoplasmic reticulum; IDA:UniProtKB. DR GO; GO:0044167; C:host cell endoplasmic reticulum membrane; IEA:UniProtKB-SubCell. DR GO; GO:0044174; C:host cell endosome; IEA:UniProtKB-SubCell. DR GO; GO:0044187; C:host cell lysosome; IEA:UniProtKB-SubCell. DR GO; GO:0020002; C:host cell plasma membrane; IEA:UniProtKB-SubCell. DR GO; GO:0005886; C:plasma membrane; IDA:ComplexPortal. DR GO; GO:0055036; C:virion membrane; TAS:Reactome. DR GO; GO:0005891; C:voltage-gated calcium channel complex; IPI:ComplexPortal. DR GO; GO:0008076; C:voltage-gated potassium channel complex; IPI:ComplexPortal. DR GO; GO:0042802; F:identical protein binding; IPI:IntAct. DR GO; GO:0140677; F:molecular function activator activity; IMP:DisProt. DR GO; GO:0005216; F:monoatomic ion channel activity; IEA:UniProtKB-KW. DR GO; GO:0140883; P:induction by virus of host reticulophagy; IDA:UniProtKB. DR GO; GO:0098662; P:inorganic cation transmembrane transport; IDA:ComplexPortal. DR GO; GO:0051259; P:protein complex oligomerization; IEA:UniProtKB-KW. DR GO; GO:0039707; P:virus-mediated pore formation in host cell membrane; IEA:UniProtKB-KW. DR CDD; cd21648; SARS-CoV-like_ORF3a; 1. DR DisProt; DP03003; -. DR InterPro; IPR046446; a/bCoV_VIROPORIN_3A-like_CD. DR InterPro; IPR046445; a/bCoV_VIROPORIN_3A-like_TM. DR InterPro; IPR024407; Protein_3a_bCoV. DR Pfam; PF11289; bCoV_viroporin; 1. DR PROSITE; PS51967; COV_VIROPORIN_3A_CD; 1. DR PROSITE; PS51966; COV_VIROPORIN_3A_TM; 1. PE 1: Evidence at protein level; KW 3D-structure; Activation of host autophagy by virus; Glycoprotein; KW Host cell membrane; Host cytoplasm; Host endoplasmic reticulum; KW Host endosome; Host lysosome; Host membrane; Host-virus interaction; KW Ion channel; Ion transport; Membrane; Reference proteome; Secreted; KW Transmembrane; Transmembrane helix; Transport; Viral ion channel; Virion. FT CHAIN 1..275 FT /note="ORF3a protein" FT /id="PRO_0000449650" FT TOPO_DOM 1..42 FT /note="Extracellular" FT /evidence="ECO:0000269|PubMed:34158638" FT TRANSMEM 43..61 FT /note="Helical" FT /evidence="ECO:0000269|PubMed:34158638" FT TOPO_DOM 62..67 FT /note="Cytoplasmic" FT /evidence="ECO:0000269|PubMed:34158638" FT TRANSMEM 68..93 FT /note="Helical" FT /evidence="ECO:0000269|PubMed:34158638" FT TOPO_DOM 94..101 FT /note="Extracellular" FT /evidence="ECO:0000269|PubMed:34158638" FT TRANSMEM 102..126 FT /note="Helical" FT /evidence="ECO:0000269|PubMed:34158638" FT TOPO_DOM 127..275 FT /note="Cytoplasmic" FT /evidence="ECO:0000269|PubMed:34158638" FT DOMAIN 33..141 FT /note="CoV 3a-like viroporin TM" FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01311" FT DOMAIN 145..237 FT /note="CoV 3a-like viroporin CD" FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01312" FT REGION 1..39 FT /note="Disordered" FT /evidence="ECO:0000305|PubMed:35108439" FT REGION 239..275 FT /note="Disordered" FT /evidence="ECO:0000305|PubMed:35108439" FT SITE 133 FT /note="Involved in polymerization" FT /evidence="ECO:0000250|UniProtKB:P59632" FT CARBOHYD 32 FT /note="O-linked (GalNAc...) threonine; by host" FT /evidence="ECO:0000250|UniProtKB:P59632" FT CARBOHYD 34 FT /note="O-linked (GalNAc...) threonine; by host" FT /evidence="ECO:0000255" FT VARIANT 26 FT /note="S -> L (in strain: Delta/B.1.617.2 and Kappa/ FT B.1.617.1)" FT /evidence="ECO:0000305" FT VARIANT 42 FT /note="P -> L (in strain: Iota/B.1.526)" FT /evidence="ECO:0000305" FT VARIANT 57 FT /note="Q -> H (in strain: Beta/B.1.351, Epsilon/B.1.429, FT Iota/B.1.526 and Mu/B.1.621)" FT /evidence="ECO:0000305" FT VARIANT 171 FT /note="S -> L (in strain: Beta/B.1.351)" FT /evidence="ECO:0000305" FT VARIANT 223 FT /note="T -> I (in strain: Omicron/BA.2, Omicron/BA.2.12.1, FT Omicron/BA.2.75, Omicron/BA.4, Omicron/BA.5, Omicron/ FT BQ.1.1, Omicron/XBB.1.5, Omicron/EG.5.1)" FT /evidence="ECO:0000305" FT VARIANT 253 FT /note="S -> P (in strain: Gamma/P.1)" FT /evidence="ECO:0000305" FT VARIANT 257 FT /note="Missing (in strain: Mu/B.1.621)" FT /evidence="ECO:0000305" FT MUTAGEN 1..41 FT /note="Missing: Partial loss of Ca(2+) and NMDG(+) FT permeability. Increased localization at host plasma FT membrane." FT /evidence="ECO:0000269|PubMed:34158638" FT MUTAGEN 57..58 FT /note="QS->EL: Partial loss of Ca(2+) and NMDG(+) FT permeability." FT /evidence="ECO:0000269|PubMed:34158638" FT MUTAGEN 57 FT /note="Q->H: No effect on ion permeability." FT /evidence="ECO:0000269|PubMed:34158638" FT MUTAGEN 116 FT /note="Q->L: Partial loss of Ca(2+) and NMDG(+) FT permeability." FT /evidence="ECO:0000269|PubMed:34158638" FT HELIX 44..60 FT /evidence="ECO:0007829|PDB:7KJR" FT HELIX 68..99 FT /evidence="ECO:0007829|PDB:7KJR" FT HELIX 103..105 FT /evidence="ECO:0007829|PDB:7KJR" FT HELIX 106..133 FT /evidence="ECO:0007829|PDB:7KJR" FT HELIX 137..140 FT /evidence="ECO:0007829|PDB:7KJR" FT STRAND 144..150 FT /evidence="ECO:0007829|PDB:7KJR" FT STRAND 155..160 FT /evidence="ECO:0007829|PDB:7KJR" FT STRAND 165..172 FT /evidence="ECO:0007829|PDB:7KJR" FT STRAND 183..186 FT /evidence="ECO:0007829|PDB:7KJR" FT STRAND 189..192 FT /evidence="ECO:0007829|PDB:7KJR" FT STRAND 199..204 FT /evidence="ECO:0007829|PDB:7KJR" FT STRAND 209..218 FT /evidence="ECO:0007829|PDB:7KJR" FT HELIX 220..223 FT /evidence="ECO:0007829|PDB:7KJR" FT STRAND 228..235 FT /evidence="ECO:0007829|PDB:7KJR" SQ SEQUENCE 275 AA; 31123 MW; 4688E6D477E031C4 CRC64; MDLFMRIFTI GTVTLKQGEI KDATPSDFVR ATATIPIQAS LPFGWLIVGV ALLAVFQSAS KIITLKKRWQ LALSKGVHFV CNLLLLFVTV YSHLLLVAAG LEAPFLYLYA LVYFLQSINF VRIIMRLWLC WKCRSKNPLL YDANYFLCWH TNCYDYCIPY NSVTSSIVIT SGDGTTSPIS EHDYQIGGYT EKWESGVKDC VVLHSYFTSD YYQLYSTQLS TDTGVEHVTF FIYNKIVDEP EEHVQIHTID GSSGVVNPVM EPIYDEPTTT TSVPL //