Conserved Protein Domain Family
TM_Y_CoV_Nsp3_C

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cd21686: TM_Y_CoV_Nsp3_C 
C-terminus of coronavirus non-structural protein 3, including transmembrane and Y domains
This model represents the C-terminus of non-structural protein 3 (Nsp3) from alpha-, beta-, gamma-, and deltacoronavirus, including highly pathogenic betacoronaviruses such as Severe acute respiratory syndrome-related coronavirus (SARS-CoV), SARS-CoV2 (also called 2019 novel CoV or 2019-nCoV), and Middle East respiratory syndrome-related (MERS) CoV. This conserved C-terminus includes two transmembrane (TM) regions TM1 and TM2, an ectodomain (3Ecto) between the TM1 and TM2 that is glycosylated and located on the lumenal side of the ER, an amphiphatic region (AH1) that is not membrane-spanning, and a large Y domain of approximately 370 residues. Nsp3 is a large multi-functional multi-domain protein that is an essential component of the replication/transcription complex (RTC), which carries out RNA synthesis, RNA processing, and interference with the host cell innate immune system. In SARS-CoV and murine hepatitis virus (MHV), the TM1, 3Ecto and TM2 domains are important for the papain-like protease (PL2pro) domain to process Nsp3-Nsp4 cleavage. It has also been shown that the interaction of 3Ecto with the lumenal loop of Nsp4 is essential for ER rearrangements in cells infected with SARS-CoV or MHV. The Y domain, located at the cytosolic side of the ER, consists of the Y1 and CoV-Y subdomains, which are conserved in nidovirus and coronavirus, respectively. Functional information about the Y domain is limited; it has been shown that Nsp3 binding to Nsp4 is less efficient without the Y domain.
Statistics
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PSSM-Id: 409657
Aligned: 4 rows
Threshold Bit Score: 599.947
Created: 27-Apr-2020
Updated: 25-Oct-2021
Structure
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Aligned Rows:
 
TM1 [structuralTM2 [structural
Feature 1:TM1 [structural motif]
Evidence:

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1      ######################                                                          
QHD43415  2232 WFLLLSVCLGSLIYSTAALGVLm-------------SNLGMPSYCTGYREGYLNSTnv-tiATYCTgSIPCSVCLSGLDS 2297 Severe acute res...
AXR85430  1741 VASYRSVLCKVVFATLLIVWFIytsnpvmftgtrvlDFLFEGSLCGPYNDYGKDSFd---vLRYCGdDFTCRVCLHDKDS 1817 Infectious bronc...
QDH76194  1505 LYYSAQTLFVSLAPFLMLPAVVsll--------nsgYTIGTYLYAKTGWPCNYNATqhfdyNSYCAgDLVCQACFDGQDS 1576 Porcine deltacor...
SNQ27886  2015 FFKLKLYWFKVLGKFSLGIYALyallf-----mtirFTPIGGPVCDDVVAGYANSSfd--kNEYCN-SVICKVCLYGYQE 2086 Porcine epidemic...
Feature 1                                                                                      
QHD43415  2298 LDTYPSletiqitissfkwdltafglvaewflayilftrFFYVLGLAAIMQLFFSYFAVHFIs----------------- 2360 Severe acute res...
AXR85430  1818 LHLYKHaysveqvykd-------------avsgisfnwnWLYLVFLILFVKPVAGFVIICYCvkylvls------stvlq 1878 Infectious bronc...
QDH76194  1577 LHLYPHlrvnqqplqt-------------tdytvyalslILLLANMTLVMGTLIVTFFVNFYgv---------------- 1627 Porcine deltacor...
SNQ27886  2087 LSDFSHtqvvw-----------------------qhlrdPLIGNVMPFFYLAFLAIFGGVYVkaitlyficqylnilgvf 2143 Porcine epidemic...
Feature 1                                                                                      
QHD43415  2361 --NSWLMWLIInlvqmapISAMVRMYIFFasFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGVRRSFYVYA 2438 Severe acute res...
AXR85430  1879 tgVGFVDWFIQtvf--thFNFMGAGFYFW--LFYKLYIQVHHILYCKDITCEVCKRVARSNRHEVGVVVGGRKQIVHVYT 1954 Infectious bronc...
QDH76194  1628 -qIPFYGTLLIdy----qSALMMTFSVYY--FYKVMKFFRHLTHGCKIPTCMVCAKLRTPPTITVETVVQGRKYPSVIET 1700 Porcine deltacor...
SNQ27886  2144 lgLQQSIWFLQlv---pfDVFGDEIVVFFi-VTRVLMFLKHVFFGCDKASCVACSRSARLKRVPVQTIFQGTSKSFYVHA 2219 Porcine epidemic...
Feature 1                                                                                      
QHD43415  2439 NGGkgFCKLHNWNCVNCDTFCAGsTFISDEVARDLSlqfKRPINPTDQSSYIVDSVtvkng--sihlyFDKAGQKt---- 2512 Severe acute res...
AXR85430  1955 NSGynFCKRHNWYCRNCDVYGHQnTFMSPEVAGELSeklKRHVKPTAHAYHVVDDAcvv-------ddFVNLKYKaatp- 2026 Infectious bronc...
QDH76194  1701 NGGftICKEHNFYCKDCSLQTPG-TFIPTEAIESLSratRLSVKPTAPAFLLARDVecqt-----dvvVARAMHNq---- 1770 Porcine deltacor...
SNQ27886  2220 NGGskFCKKHNFFCLNCDSYGPGcTFINDVIATEVGnvvKLNVQPTGPATILIDKVefsngfyylysgDTFWKYNfditd 2299 Porcine epidemic...
Feature 1                                                                                      
QHD43415  2513 ---YERHSLSHFVNl-----------------DNLRANNTkgslpinvivfdgkSKCEEss-----------------aK 2555 Severe acute res...
AXR85430  2027 gkdSAPPAVKCFSVt-----------------DFLKKAVFlk----------daLKCEQisndsfivcntqsahsleeaK 2079 Infectious bronc...
QDH76194  1771 ---NAHVCISKYSDirtvdqllkptplfsytpDVIIAADF--------------DNRGSlk----------------taK 1817 Porcine deltacor...
SNQ27886  2300 skyTCKESLKNCSIi----------------tDFIVFNNNg-------------SNVNQv-------------------K 2331 Porcine epidemic...
Feature 1                                                                                      
QHD43415  2556 SASVYYSQLMCQPILLLDQALvsdvgdsaevavk----mfdayvntfsstfNVPMEKlktlvataeaelaknvsldnvls 2631 Severe acute res...
AXR85430  2080 NAAIYYAQYLCKPILILDQALyer-------------------------lvVEPVSKdvvdkvcnilsn------iisvd 2128 Infectious bronc...
QDH76194  1818 ELAVVLSMDLKRTIIIIDQAYsrpidnyq--------------evasriekYYPVAKitptgd----------------- 1866 Porcine deltacor...
SNQ27886  2332 NACVYFSQMLCKPVKLVDSALlaslsvdfgaslhsafvsvlsnsfgkdlssCNDMQDck--------------------- 2390 Porcine epidemic...
Feature 1                                                                                      
QHD43415  2632 tfisaaRQGFvd-------sDVETKDVVEclk-lsHQSDIEVTGDSCNNyMLTYNKVENmtprdlgac-idcsarhiNAQ 2702 Severe acute res...
AXR85430  2129 taalnyKAGTirdallsvtkDEEAVDMAIf----cHNHDVEYTGDGFTNvISSYGIDTGkltprdrg--flvnadasIAN 2202 Infectious bronc...
QDH76194  1867 -iftdiKQAT----------NGQASDSAInaavlaVQRGLDFTIDNPNNiLPHYAFDFStltaedq----stilesgCAK 1931 Porcine deltacor...
SNQ27886  2391 -----sTLGF----------DDVPLDTFNaavaeaHRYDVLLTDMSFNNfTTSYAKPEEklpvhdiatcmrvgakivNHN 2455 Porcine epidemic...
Feature 1                                                                    
QHD43415  2703 VAKSHNIALIWNvkd-fmSLSEQLRKQIRSAAKKNNLpFKLTCATTRQVVNV-VTTKIALKG 2762 Severe acute respiratory syndrome ...
AXR85430  2203 LRVKNAPPVVWKfsd-liKLSDSCLKYLISATVKSGSrFFITRSGAKQIFSCsTQKLLVEKK 2263 Infectious bronchitis virus
QDH76194  1932 GNLKGTNVGVVLsaslvtRLSQQAIRVIANAASRNGVtCAVTPSTLVMRGNIaTQPLTRIKA 1993 Porcine deltacoronavirus
SNQ27886  2456 VLVKDSIPVVWLvrd-fiALSEETRKYIIRTTKVKGItFMLTFNDCRMHTTI-PTVCIANKK 2515 Porcine epidemic diarrhea virus

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