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Conserved domains on  [gi|693764262|ref|YP_009072441|]
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ORF4 protein [Bat Hp-betacoronavirus/Zhejiang2013]

Protein Classification

ORF3a domain-containing protein( domain architecture ID 1776289)

ORF3a domain-containing protein similar to the accessory protein ORF3a of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that promotes membrane rearrangement and cell death; it induces vesicle formation and is necessary for SARS-CoV-induced Golgi fragmentation

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SARS-CoV-like_ORF3a super family cl40628
accessory protein ORF3a of severe acute respiratory syndrome-associated coronavirus and ...
 47-244 2.93e-03

accessory protein ORF3a of severe acute respiratory syndrome-associated coronavirus and similar proteins from related betacoronavirus; This model represents the accessory protein ORF3a of Severe Acute Respiratory Syndrome-associated coronavirus (SARS-CoV), SARS-COV-2 (also called 2019 novel coronavirus or 2019-nCoV), and related betacoronaviruses in the Sarbecovirus subgenus (B lineage). There are five essential genes in CoVs that result in the following gene products: Spike (S) protein, Membrane (M) glycoprotein, Nucleocapsid (N), Envelope (E) protein, and replicase/protease polyproteins (ORF1ab); all are required to produce a structurally complete viral particle. In addition, CoV genomes also contain ORFs coding for accessory proteins that are specific for certain CoV lineages or for a particular CoV. In general, CoV accessory proteins are considered to be dispensable for viral replication; however, several accessory proteins have been shown to exhibit functions in virus-host interactions during CoV infection. SARS-CoV mRNA 3 encodes the distinct proteins ORF3a and ORF3b, which are translated in different reading frames. Accessory protein ORF3a, also called protein 3a and protein X1, is the largest ORF protein in SARS-CoV. It is also called accessory protein 3 or protein 3 in some bat coronaviruses. SARS-CoV ORF3a promotes membrane rearrangement and cell death; it induces vesicle formation and is necessary for SARS-CoV-induced Golgi fragmentation. It has also been found to activate NF-kappaB and the NLRP3 inflammasome by promoting TNF receptor-associated factor 3 (TRAF3)-dependent ubiquitination of p105 and ASC (apoptosis-associated speck-like protein containing a caspase recruitment domain). The cytoplasmic domain of SARS-CoV ORF3a, composed of amino acids at the C-terminal region, has sequence similarity to a calcium pump present in Plasmodium falciparum and has been shown to bind calcium in vitro. SARS-CoV-2 3a is able to form ion channels; it is a Class IIIA viroporin, having 3 transmembrane helices per protomer and a lumenal amino terminus and cytosolic carboxyl terminus. It can form dimers, tetramers, and potentially higher order oligomers. It has been shown to form cation channels with modest selectivity for Ca2+ and K+ over Na+.


The actual alignment was detected with superfamily member cd21648:

Pssm-ID: 477412  Cd Length: 269  Bit Score: 37.90  E-value: 2.93e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 693764262  47 LCIFLVIYLICYFLRTdsFIAVVFKYLagLLTGGflclglfLDTPTLLLKATIGVVLFMFSLGFICRITLAIRCKSLVPL 126
Cdd:cd21648   67 LALYKGIQLVCNLLLL--FVTIYSHLL--LLAAG-------MEAQFLYIYALIYILQIVSFCRFIMRCWLCWKCKSKNPL 135

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 693764262 127 CADDDCFVNYNAGGKTYCMPFdpNEPYLTLVVHQ-NGIT---------CGSYKLYGDVSIADRIYLVTLTKSVPYSL--- 193
Cdd:cd21648  136 LYDANYFVCWHTHNYDYCIPY--NSVTDTIVVTAgDGIStpklkedyqIGGYSEDWHSGVKDYVVVHGYFTEVYYQLest 213

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 693764262 194 QNIFDAELCTIAFYI-----ADCAVIEDHTTAGKTPRLELKSDPIYEVPCATIDVP 244
Cdd:cd21648  214 QISTDTGIENATFFIfnklvKDPPNVQIHTIDGSSGVVNPAMDPIYDEPTTTTSVP 269
 
Name Accession Description Interval E-value
SARS-CoV-like_ORF3a cd21648
accessory protein ORF3a of severe acute respiratory syndrome-associated coronavirus and ...
 47-244 2.93e-03

accessory protein ORF3a of severe acute respiratory syndrome-associated coronavirus and similar proteins from related betacoronavirus; This model represents the accessory protein ORF3a of Severe Acute Respiratory Syndrome-associated coronavirus (SARS-CoV), SARS-COV-2 (also called 2019 novel coronavirus or 2019-nCoV), and related betacoronaviruses in the Sarbecovirus subgenus (B lineage). There are five essential genes in CoVs that result in the following gene products: Spike (S) protein, Membrane (M) glycoprotein, Nucleocapsid (N), Envelope (E) protein, and replicase/protease polyproteins (ORF1ab); all are required to produce a structurally complete viral particle. In addition, CoV genomes also contain ORFs coding for accessory proteins that are specific for certain CoV lineages or for a particular CoV. In general, CoV accessory proteins are considered to be dispensable for viral replication; however, several accessory proteins have been shown to exhibit functions in virus-host interactions during CoV infection. SARS-CoV mRNA 3 encodes the distinct proteins ORF3a and ORF3b, which are translated in different reading frames. Accessory protein ORF3a, also called protein 3a and protein X1, is the largest ORF protein in SARS-CoV. It is also called accessory protein 3 or protein 3 in some bat coronaviruses. SARS-CoV ORF3a promotes membrane rearrangement and cell death; it induces vesicle formation and is necessary for SARS-CoV-induced Golgi fragmentation. It has also been found to activate NF-kappaB and the NLRP3 inflammasome by promoting TNF receptor-associated factor 3 (TRAF3)-dependent ubiquitination of p105 and ASC (apoptosis-associated speck-like protein containing a caspase recruitment domain). The cytoplasmic domain of SARS-CoV ORF3a, composed of amino acids at the C-terminal region, has sequence similarity to a calcium pump present in Plasmodium falciparum and has been shown to bind calcium in vitro. SARS-CoV-2 3a is able to form ion channels; it is a Class IIIA viroporin, having 3 transmembrane helices per protomer and a lumenal amino terminus and cytosolic carboxyl terminus. It can form dimers, tetramers, and potentially higher order oligomers. It has been shown to form cation channels with modest selectivity for Ca2+ and K+ over Na+.


Pssm-ID: 439223  Cd Length: 269  Bit Score: 37.90  E-value: 2.93e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 693764262  47 LCIFLVIYLICYFLRTdsFIAVVFKYLagLLTGGflclglfLDTPTLLLKATIGVVLFMFSLGFICRITLAIRCKSLVPL 126
Cdd:cd21648   67 LALYKGIQLVCNLLLL--FVTIYSHLL--LLAAG-------MEAQFLYIYALIYILQIVSFCRFIMRCWLCWKCKSKNPL 135

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 693764262 127 CADDDCFVNYNAGGKTYCMPFdpNEPYLTLVVHQ-NGIT---------CGSYKLYGDVSIADRIYLVTLTKSVPYSL--- 193
Cdd:cd21648  136 LYDANYFVCWHTHNYDYCIPY--NSVTDTIVVTAgDGIStpklkedyqIGGYSEDWHSGVKDYVVVHGYFTEVYYQLest 213

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 693764262 194 QNIFDAELCTIAFYI-----ADCAVIEDHTTAGKTPRLELKSDPIYEVPCATIDVP 244
Cdd:cd21648  214 QISTDTGIENATFFIfnklvKDPPNVQIHTIDGSSGVVNPAMDPIYDEPTTTTSVP 269
 
Name Accession Description Interval E-value
SARS-CoV-like_ORF3a cd21648
accessory protein ORF3a of severe acute respiratory syndrome-associated coronavirus and ...
 47-244 2.93e-03

accessory protein ORF3a of severe acute respiratory syndrome-associated coronavirus and similar proteins from related betacoronavirus; This model represents the accessory protein ORF3a of Severe Acute Respiratory Syndrome-associated coronavirus (SARS-CoV), SARS-COV-2 (also called 2019 novel coronavirus or 2019-nCoV), and related betacoronaviruses in the Sarbecovirus subgenus (B lineage). There are five essential genes in CoVs that result in the following gene products: Spike (S) protein, Membrane (M) glycoprotein, Nucleocapsid (N), Envelope (E) protein, and replicase/protease polyproteins (ORF1ab); all are required to produce a structurally complete viral particle. In addition, CoV genomes also contain ORFs coding for accessory proteins that are specific for certain CoV lineages or for a particular CoV. In general, CoV accessory proteins are considered to be dispensable for viral replication; however, several accessory proteins have been shown to exhibit functions in virus-host interactions during CoV infection. SARS-CoV mRNA 3 encodes the distinct proteins ORF3a and ORF3b, which are translated in different reading frames. Accessory protein ORF3a, also called protein 3a and protein X1, is the largest ORF protein in SARS-CoV. It is also called accessory protein 3 or protein 3 in some bat coronaviruses. SARS-CoV ORF3a promotes membrane rearrangement and cell death; it induces vesicle formation and is necessary for SARS-CoV-induced Golgi fragmentation. It has also been found to activate NF-kappaB and the NLRP3 inflammasome by promoting TNF receptor-associated factor 3 (TRAF3)-dependent ubiquitination of p105 and ASC (apoptosis-associated speck-like protein containing a caspase recruitment domain). The cytoplasmic domain of SARS-CoV ORF3a, composed of amino acids at the C-terminal region, has sequence similarity to a calcium pump present in Plasmodium falciparum and has been shown to bind calcium in vitro. SARS-CoV-2 3a is able to form ion channels; it is a Class IIIA viroporin, having 3 transmembrane helices per protomer and a lumenal amino terminus and cytosolic carboxyl terminus. It can form dimers, tetramers, and potentially higher order oligomers. It has been shown to form cation channels with modest selectivity for Ca2+ and K+ over Na+.


Pssm-ID: 439223  Cd Length: 269  Bit Score: 37.90  E-value: 2.93e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 693764262  47 LCIFLVIYLICYFLRTdsFIAVVFKYLagLLTGGflclglfLDTPTLLLKATIGVVLFMFSLGFICRITLAIRCKSLVPL 126
Cdd:cd21648   67 LALYKGIQLVCNLLLL--FVTIYSHLL--LLAAG-------MEAQFLYIYALIYILQIVSFCRFIMRCWLCWKCKSKNPL 135

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 693764262 127 CADDDCFVNYNAGGKTYCMPFdpNEPYLTLVVHQ-NGIT---------CGSYKLYGDVSIADRIYLVTLTKSVPYSL--- 193
Cdd:cd21648  136 LYDANYFVCWHTHNYDYCIPY--NSVTDTIVVTAgDGIStpklkedyqIGGYSEDWHSGVKDYVVVHGYFTEVYYQLest 213

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 693764262 194 QNIFDAELCTIAFYI-----ADCAVIEDHTTAGKTPRLELKSDPIYEVPCATIDVP 244
Cdd:cd21648  214 QISTDTGIENATFFIfnklvKDPPNVQIHTIDGSSGVVNPAMDPIYDEPTTTTSVP 269
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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