AP3A_SARS2
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 03-AUG-2022, entry version 12.
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.
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 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 (viroporin) localized at endosomes and lysosomes, that may induce
CC deacidification of lysosomes, allowing safe egress of virions via
CC lysosomal trafficking (PubMed:33157038,
CC PubMed:33422265,PubMed:34158638). Also blocks autolysosomes formation
CC by binding and sequestering the host component VPS39 for homotypic
CC fusion and protein sorting (HOPS) on late endosomes. This prevents
CC fusion of autophagosomes with lysosomes, disrupting autophagy and
CC facilitating virus egress (PubMed:33422265).
CC {ECO:0000269|PubMed:33157038, ECO:0000269|PubMed:33422265,
CC ECO:0000269|PubMed:34158638}.
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).
CC {ECO:0000250|UniProtKB:P59632, ECO:0000269|PubMed:33422265,
CC ECO:0000269|PubMed:34158638}.
CC -!- INTERACTION:
CC P0DTC3; P0DTC3: 3a; NbExp=2; IntAct=EBI-25475894, EBI-25475894;
CC P0DTC3; Q9P2Y5: UVRAG; Xeno; NbExp=6; IntAct=EBI-25475894, EBI-2952704;
CC P0DTC3; Q96JC1: VPS39; Xeno; NbExp=15; IntAct=EBI-25475894, EBI-1050197;
CC P0DTC3; P49754: VPS41; Xeno; NbExp=4; IntAct=EBI-25475894, EBI-2130459;
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}. 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}.
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DR EMBL; MN908947; QHD43417.1; -; Genomic_RNA.
DR RefSeq; YP_009724391.1; NC_045512.2.
DR PDB; 6XDC; EM; 2.90 A; A/B=1-275.
DR PDB; 7KJR; EM; 2.08 A; A/B=1-275.
DR PDBsum; 6XDC; -.
DR PDBsum; 7KJR; -.
DR SMR; P0DTC3; -.
DR BioGRID; 4383868; 1113.
DR ComplexPortal; CPX-6098; SARS-CoV-2 3a complex.
DR IntAct; P0DTC3; 442.
DR TCDB; 1.A.57.1.5; the human sars coronavirus viroporin (sars-vp).
DR GlyGen; P0DTC3; 2 sites.
DR DNASU; 43740569; -.
DR GeneID; 43740569; -.
DR KEGG; vg:43740569; -.
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-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: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:0044385; C:integral to membrane of host cell; IEA:UniProtKB-KW.
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:0005216; F:ion channel activity; IEA:UniProtKB-KW.
DR GO; GO:0098662; P:inorganic cation transmembrane transport; IDA:ComplexPortal.
DR GO; GO:0039707; P:pore formation by virus in membrane of host cell; IEA:UniProtKB-KW.
DR GO; GO:0051259; P:protein complex oligomerization; IEA:UniProtKB-KW.
DR CDD; cd21648; SARS-CoV-like_ORF3a; 1.
DR DisProt; DP03003; -.
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; Glycoprotein; Host cell membrane; Host cytoplasm;
KW Host endosome; Host lysosome; Host membrane; Ion channel; Ion transport;
KW Membrane; Reference proteome; Secreted; Transmembrane; Transmembrane helix;
KW 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 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.1621)"
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.4, Omicron/BA.5)"
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
