6VSB,5X58,6VSB,6VSB,6NB6,6CRW,6CRV,5WRG,6ACC


Conserved Protein Domain Family
SARS-CoV-like_Spike_SD1-2_S1-S2_S2

?
cd22378: SARS-CoV-like_Spike_SD1-2_S1-S2_S2 
SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from SARS-CoV-2 (COVID-19) and related betacoronaviruses in the B lineage
This group contains the SD-1 and SD-2 subdomains of the S1 subunit C-terminal domain (C-domain), the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from betacoronaviruses in the sarbecovirus subgenus (B lineage), including highly pathogenic human CoVs such as Severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV), and SARS-CoV-2 (also known as a 2019 novel coronavirus or 2019-nCoV). The CoV S protein is an envelope glycoprotein that plays a very important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains the coronavirus fusion machinery and is primarily alpha-helical. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-domain. The S1 C-domain also contains two subdomains (SD-1 and SD-2), which connect the S1 and S2 subunits. Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs, including SARS-CoV-2, SARS-CoV and MERS-CoV use the C-domain to bind their receptors. The S2 subunit comprises the fusion peptide (FP), a second proteolytic site (S2'), followed by an internal fusion peptide (IFP) and two heptad-repeat domains (HR1 and HR2) preceding the transmembrane domain (TM). After binding of the S1 subunit RBD on the virion to its receptor on the target cell, the HR1 and HR2 domains interact with each other to form a six-helix bundle (6-HB) fusion core, bringing viral and cellular membranes into close proximity for fusion and infection. In order to catalyze the membrane fusion reaction, CoV S needs to be primed through cleavage at the S1/S2 and S2' sites. Notably, SARS-CoV-2 has a functional polybasic (furin) cleavage site through the insertion of PRRAR*SV (* indicates the cleavage site) at the S1/S2 interface, which is absent in SARS-CoV and other SARS-related coronaviruses. The region modeled in this cd (SD-1 and SD-2, the S1/S2 cleavage region, and the S2 fusion subunit) plays an essential role in viral entry by initiating fusion of the viral and cellular membranes.
Statistics
?
PSSM-Id: 411965
Aligned: 22 rows
Threshold Bit Score: 1370.07
Created: 20-May-2020
Updated: 25-Oct-2021
Structure
?
Program:
Drawing:
Aligned Rows:
  next features
Conserved site includes 12 residues -Click on image for an interactive view with Cn3D
Feature 1:N-linked glycosylation sites [posttranslational modification site]
Evidence:
  • Comment:betacoronavirus Spike (S) proteins typically contain 22-30 N-linked glycosylation sites per protomer, depending on the species
  • Structure:6VSB; SARS-CoV-2 S protein possesses a total of 22 N-linked glycan sites per protomer, which likely play a role in protein folding and immune evasion, with each trimer displaying 66 N-linked glycosylation sites.
    View structure with Cn3D

Sequence Alignment
?
Format: Row Display: Color Bits: Type Selection:
Feature 1                                                                  #            #      
6VSB_A     543 FNGLTGTGVLTESNKKFlpFQQFGRDIaDTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPV 622  Severe acute res...
QJX68370   543 FNGLTGTGVLTESNKKFlpFQQFGRDIaDTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPV 622  Severe acute res...
QIQ54048   543 FNGLTGTGVLTTSKKQFlpFQQFGRDIsDTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPM 622  Pangolin coronav...
AVP78042   519 FNGLKGTGVLTDSSKRFqsFQQFGKDAsDFIDSVRDPQTLEILDITPCSFGGVSVITPGTNTSSEVAVLYQDVNCTDVPT 598  Bat SARS-like co...
Q3LZX1     516 FNGLKGTGVLTSSSKRFqsFQQFGRDTsDFTDSVRDPQTLEILDISPCSFGGVSVITPGTNASSEVAVLYQDVNCTDVPT 595  Bat SARS coronav...
Q3I5J5     515 FNGLKGTGVLTESSKRFqsFQQFGRDTsDFTDSVRDPQTLEILDISPCSFGGVSVITPGTNASSEVAVLYQDVNCTDVPA 594  Bat SARS CoV Rp3...
Q0Q475     515 FNGLRGTGVLTTSSKRFqsFQQFGRDTsDFTDSVRDPQTLEILDISPCSFGGVSVITPGTNASSEVAVLYQDVNCTDVPT 594  Bat CoV 279/2005
AKZ19087   515 FNGFKGTGVLTDSSKTFqsFQQFGRDAsDFTDSVRDPKTLQILDISPCSFGGVSVITPGTNTSSAVAVLYQDVNCTDVPK 594  Bat SARS-like co...
AIA62339   515 FNGFKGTGVLTDSSKTFqsFQQFGRDAsDFTDSVRDPQTLRILDISPCSFGGVSVITPGTNTSSAVAVLYQDVNCTDVPT 594  BtRf-BetaCoV/HeN...
ALJ94036   533 FNGLTGTGVLTSSSKKFqpFQQFGRDVsDFTDSVRDPKTLEILDIAPCSYGGVSVITPGTNASNSVAVLYQDVNCTDVPT 612  SARS-like corona...
Feature 1                                          #                                           
6VSB_A     623 AIHADQLTPTWRVYST--GSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTqtnspGSASSVAsQSIIAYTMSLG 700  Severe acute res...
QJX68370   623 AIHADQLTPTWRVYST--GSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTqtnspRRARSVAsQSIIAYTMSLG 700  Severe acute res...
QIQ54048   623 AIHAEQLTPAWRVYSA--GANVFQTRAGCLVGAEHVNNSYECDIPVGAGICASYHSm----SSFRSVNqRSIIAYTMSLG 696  Pangolin coronav...
AVP78042   599 TIHADQLTPAWRIYAI--GTSVFQTQAGCLIGAEHVNASYECDIPIGAGICASYHTa----SILRSTGqKAIVAYTMSLG 672  Bat SARS-like co...
Q3LZX1     596 AIRADQLTPAWRVYST--GVNVFQTQAGCLIGAEHVNASYECDIPIGAGICASYHTa----SVLRSTGqKSIVAYTMSLG 669  Bat SARS coronav...
Q3I5J5     595 AIHADQLTPAWRVYST--GTNVFQTQAGCLIGAEHVNASYECDIPIGAGICASYHTa----STLRSVGqKSIVAYTMSLG 668  Bat SARS CoV Rp3...
Q0Q475     595 SIHADQLTPAWRVYST--GVNVFQTQAGCLIGAEHVNASYECDIPIGAGICASYHTa----SVLRSTGqKSIVAYTMSLG 668  Bat CoV 279/2005
AKZ19087   595 TIHADQLAPSWRVYTS--GPFVFQTQAGCLIGAEHVNSSYECDIPIGAGICASYHTa----SVLRSTGqKSIVAYTMSLG 668  Bat SARS-like co...
AIA62339   595 TLHADQLAPSWRVYTT--GSYVFQTQAGCLIGAEHVNASYQCDIPIGAGICASYHTa----SLLRSTGqKSIVAYTMSLG 668  BtRf-BetaCoV/HeN...
ALJ94036   613 MLHAEQISHDWRVYTFssDSNIYQTQAGCLIGAAYDNSSYECDIPIGAGICAKYGIss--nTRLRSNS-QSIVAYTMSLG 689  SARS-like corona...
Feature 1              #       #                                                               
6VSB_A     701 AENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTgIAVEQDKNTQE 780  Severe acute res...
QJX68370   701 AENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTgIAVEQDKNTQE 780  Severe acute res...
QIQ54048   697 AENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSIECSNLLLQYGSFCTQLNRALTgIAVEQDKNTQE 776  Pangolin coronav...
AVP78042   673 AENSIAYANNSIAIPTNFSISVTTEVMPVSMAKTSVDCTMYICGDSIECSNLLLQYGSFCTQLNRALSgIAIEQDKNTQE 752  Bat SARS-like co...
Q3LZX1     670 AENSIAYANNSIAIPTNFSISVTTEVMPVSMAKTAVDCTMYICGDSLECSNLLLQYGSFCTQLNRALTgIAIEQDKNTQE 749  Bat SARS coronav...
Q3I5J5     669 AENSIAYANNSIAIPTNFSISVTTEVMPVSMAKTSVDCTMYICGDSLECSNLLLQYGSFCTQLNRALSgIAIEQDKNTQE 748  Bat SARS CoV Rp3...
Q0Q475     669 AENSIAYANNSIAIPTNFSISVTTEVMPVSIAKTSVDCTMYICGDSLECSNLLLQYGSFCTQLNRALTgIAIEQDKNTQE 748  Bat CoV 279/2005
AKZ19087   669 AENSVAYANNSIAIPTNFSISVTTEVMPVSMAKTSVDCTMYICGDSAECSNLLLQYGSFCTQLNRALSgIAVEQDKNTQE 748  Bat SARS-like co...
AIA62339   669 AENSVAYANNSIAIPTNFSISVTTEVMPVSMAKTSVDCTMYICGDSLECSNLLLQYGSFCTQLNRALSgIAVEQDKNTQE 748  BtRf-BetaCoV/HeN...
ALJ94036   690 EDQSIAYSNNTIAIPMNFSISVTTEVLPVSMTKTSVDCNMYICGDSTECSNLLLQYGSFCTQLNRALAgIAVEQDRNTRD 769  SARS-like corona...
Feature 1                          #                                                           
6VSB_A     781 VFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQyGDCLGDIAARDLICAQKFNGLTV 860  Severe acute res...
QJX68370   781 VFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQyGDCLGDIAARDLICAQKFNGLTV 860  Severe acute res...
QIQ54048   777 VFAQVKQIYKTPPIKDFGGFNFLQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQyGDCLGDIAARDLICAQKFNGLTV 856  Pangolin coronav...
AVP78042   753 VFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQyGDCLGDISARDLICAQKFNGLTV 832  Bat SARS-like co...
Q3LZX1     750 VFAQVKQMYKTPAIKDFGGFNFSQILPDPSKPTKRSFIEDLLFNKVTLADAGFMKQyGDCLGDVSARDLICAQKFNGLTV 829  Bat SARS coronav...
Q3I5J5     749 VFAQVKQMYKTPAIKDFGGFNFSQILPDPSKPTKRSFIEDLLFNKVTLADAGFMKQyGECLGDISARDLICAQKFNGLTV 828  Bat SARS CoV Rp3...
Q0Q475     749 VFAQVKQMYKTPAIKDFGGFNFSQILPDPSKPTKRSFIEDLLFNKVTLADAGFMKQyGECLGDISARDLICAQKFNGLTV 828  Bat CoV 279/2005
AKZ19087   749 VFAQVKQMYKTPTLRDFGGFNFSQILPDPLKPTKRSFIEDLLYNKVTLADAGFMKQyADCLGGINARDLICAQKFNGLTV 828  Bat SARS-like co...
AIA62339   749 VFAQVKQMYKTPTIRDFGGFNFSQILPDPLKPTKRSFIEDLLYNKVTLADAGFMKQyADCLGGINARDLICAQKFNGLTV 828  BtRf-BetaCoV/HeN...
ALJ94036   770 VFAQTKAMYKTPSLKDFGGFNFSQILPDPAKPSSRSFIEDLLYNKVTLADPGFMKQyGDCLGGVNARDLICAQKFNGLTV 849  SARS-like corona...
Feature 1                                                                                      
6VSB_A     861 LPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSS 940  Severe acute res...
QJX68370   861 LPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSS 940  Severe acute res...
QIQ54048   857 LPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSS 936  Pangolin coronav...
AVP78042   833 LPPLLTDEMIAAYTAALISGTATAGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQESLTS 912  Bat SARS-like co...
Q3LZX1     830 LPPLLTDEMVAAYTAALVSGTATAGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQESLSS 909  Bat SARS coronav...
Q3I5J5     829 LPPLLTDEMIAAYTAALVSGTATAGWTFGAGSALQIPFAMQMAYRFNGIGVTQNVLYENQKQIANQFNKAISQIQESLTT 908  Bat SARS CoV Rp3...
Q0Q475     829 LPPLLTDEMIAAYTAALVSGTATAGWTFGAGSALQIPFAMQMAYRFNGIGVTQNVLYENQKQIANQFNKAISQIQESLTT 908  Bat CoV 279/2005
AKZ19087   829 LPPLLTDDMIAAYTAALISGTATAGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKQIANQFNKAITQIQESLTT 908  Bat SARS-like co...
AIA62339   829 LPPLLTDDMIAAYTAALISGTATAGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKQIANQFNKAITQIQESLTT 908  BtRf-BetaCoV/HeN...
ALJ94036   850 LPPLLTDEMIAAYTAALVSGTATAGFTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKQIANQFNKAISQIQDSLST 929  SARS-like corona...
Feature 1                                                                                      
6VSB_A     941 TASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRA 1020 Severe acute res...
QJX68370   941 TASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRA 1020 Severe acute res...
QIQ54048   937 TASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRA 1016 Pangolin coronav...
AVP78042   913 TASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRA 992  Bat SARS-like co...
Q3LZX1     910 TASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRA 989  Bat SARS coronav...
Q3I5J5     909 TSTALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRA 988  Bat SARS CoV Rp3...
Q0Q475     909 TSTALGKLQDVVNDNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRA 988  Bat CoV 279/2005
AKZ19087   909 TSTALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRA 988  Bat SARS-like co...
AIA62339   909 TSTALGKLQDVVNQNAQALNTLVKQLSSNFGAISSALNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRT 988  BtRf-BetaCoV/HeN...
ALJ94036   930 TTTALGKLQDVINQNAIALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRA 1009 SARS-like corona...
Feature 1                                                           #                       #  
6VSB_A    1021 SANLAATKMSECVLGQSKRVDFCGKGyHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGT 1100 Severe acute res...
QJX68370  1021 SANLAATKMSECVLGQSKRVDFCGKGyHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGT 1100 Severe acute res...
QIQ54048  1017 SANLAATKMSECVLGQSKRVDFCGKGyHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHEGKAHFPREGVFVSNGT 1096 Pangolin coronav...
AVP78042   993 SANLAATKMSECVLGQSKRVDFCGKGyHLMSFPQSAPHGVVFLHVTYIPSQEKNFTTAPAICHEGKAHFPREGVFVSNGT 1072 Bat SARS-like co...
Q3LZX1     990 SANLAATKMSECVLGQSKRVDFCGKGyHLMSFPQSAPHGVVFLHVTYVPSQEKNFTTAPAICHEGKAYFPREGVFVSNGT 1069 Bat SARS coronav...
Q3I5J5     989 SANLAATKMSECVLGQSKRVDFCGKGyHLMSFPQAAPHGVVFLHVTYVPSQERNFTTAPAICHEGKAYFPREGVFVSNGT 1068 Bat SARS CoV Rp3...
Q0Q475     989 SANLAATKMSECVLGQSKRVDFCGKGyHLMSFPQAAPHGVVFLHVTYVPSQERNFTTAPAICHEGKAYFPREGVFVSNGT 1068 Bat CoV 279/2005
AKZ19087   989 SANLAATKMSECVLGQSKRVDFCGKGyHLMSFPQAAPHGVVFLHVTYVPSQEKNFTTAPAICHEGKAYFPREGVFVFNGT 1068 Bat SARS-like co...
AIA62339   989 SANLAATKMSECVLGQSKRVDFCGKGyHLMSFPQSAPHGVVFLHVTYVPSQERNFTTAPAICHEGKAYFPREGVFVSNGS 1068 BtRf-BetaCoV/HeN...
ALJ94036  1010 SANIAATKMSECVLGQSKRVDFCGKGyHLMSFPQAAPHGVVFLHVTYVPSQEQNFTTAPAICHGGKAHFPREGVFVTNGT 1089 SARS-like corona...
Feature 1                                       #                       #              #       
6VSB_A    1101 HWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQ 1180 Severe acute res...
QJX68370  1101 HWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQ 1180 Severe acute res...
QIQ54048  1097 HWFITQRNFYEPQIITTDNTFVSGSCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQ 1176 Pangolin coronav...
AVP78042  1073 HWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIINNTVYDPLQPELDSFKEELDKYFKNHTSPDIDLGDISGINASVVNIQ 1152 Bat SARS-like co...
Q3LZX1    1070 SWFITQRNFYSPQLITTDNTFVSGNCDVVIGIINNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQ 1149 Bat SARS coronav...
Q3I5J5    1069 SWFITQRNFYSPQIITTDNTFVAGSCDVVIGIINNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQ 1148 Bat SARS CoV Rp3...
Q0Q475    1069 SWFITQRNFYSPQIITTDNTFVAGNCDVVIGIINNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQ 1148 Bat CoV 279/2005
AKZ19087  1069 SWFITQRNFYSPQTITTDNTFVAGNCDVVIGIINNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQ 1148 Bat SARS-like co...
AIA62339  1069 SWFITQRNFYSPQIITTDNTFVAGSCDVVIGIINNTVYDPLQPELDSFKQELDKYFKNHTSPDVDLGDISGINASVVDIQ 1148 BtRf-BetaCoV/HeN...
ALJ94036  1090 HWFITQRNFYSPQPITTDNTFVSGNCDVVIGIVNNTVYDPLQPELESFKEELDKYFKNHTSQNVSLDGLNNINASVVDIK 1169 SARS-like corona...
Feature 1                   #              
6VSB_A    1181 KEIDRLNEVAKNLNESLIDLQELGKYEQ 1208 Severe acute respiratory syndrome coronavirus 2
QJX68370  1181 KEIDRLNEVAKNLNESLIDLQELGKYEQ 1208 Severe acute respiratory syndrome coronavirus 2
QIQ54048  1177 KEIDRLNEVAKNLNESLIDLQELGKYEQ 1204 Pangolin coronavirus
AVP78042  1153 KEIDRLNEVARNLNESLIDLQELGKYEH 1180 Bat SARS-like coronavirus
Q3LZX1    1150 KEIDRLNEVAKNLNESLIDLQELGKYEQ 1177 Bat SARS coronavirus HKU3
Q3I5J5    1149 KEIDRLNEVAKNLNESLIDLQELGKYEQ 1176 Bat SARS CoV Rp3/2004
Q0Q475    1149 KEIDRLNEVAKNLNESLIDLQELGKYEQ 1176 Bat CoV 279/2005
AKZ19087  1149 KEIDRLNEVAKNLNDSLIDLQELGKYEQ 1176 Bat SARS-like coronavirus YNLF_34C
AIA62339  1149 KEIDRLNEVAKNLNESLIDLQELGKYEQ 1176 BtRf-BetaCoV/HeN2013
ALJ94036  1170 KEIEHLNEIAKSLNESLIDLQELGKYEQ 1197 SARS-like coronavirus BatCoV/BB9904/BGR/2008

| Disclaimer | Privacy statement | Accessibility |
NCBI Home NCBI Search NCBI SiteMap