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Conserved domains on  [gi|47605755|sp|Q9UQF0|]
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RecName: Full=Syncytin-1; AltName: Full=Endogenous retrovirus group W member 1; AltName: Full=Env-W; AltName: Full=Envelope polyprotein gPr73; AltName: Full=Enverin; AltName: Full=HERV-7q Envelope protein; AltName: Full=HERV-W envelope protein; AltName: Full=HERV-W_7q21.2 provirus ancestral Env polyprotein; AltName: Full=Syncytin; Contains: RecName: Full=Surface protein; Short=SU; AltName: Full=gp50; Contains: RecName: Full=Transmembrane protein; Short=TM; AltName: Full=gp24; Flags: Precursor

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
TLV_coat super family cl27694
ENV polyprotein (coat polyprotein);
22-477 1.83e-55

ENV polyprotein (coat polyprotein);


The actual alignment was detected with superfamily member pfam00429:

Pssm-ID: 306850  Cd Length: 560  Bit Score: 195.40  E-value: 1.83e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47605755    22 PPPCRCMTSSSPYQEFLWRMQRPGNIDAPSYRSL----SKGTPTFTA-HTHMPRNCYHSATLCMHANTHYWTGK------ 90
Cdd:pfam00429  62 CSGCPDLSAYLTDQSLWPPCVTPPKRTPHANGSFyvcpGECRTRANRrHCGGYSSCYCCSWGCETTGCTYWTPAsswdyi 141
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47605755    91 ----------------------MINPSCPGGLGVTVCWTyftQTGMSDGGGVQDQAREKHVKEVISQLTRVHGTSSPYKG 148
Cdd:pfam00429 142 tvswnktsstvnctqegscnplILHFTDCGKKATTLTWG---LRLYVSGYDPLDTFRIRLKITTLNEVLRDQKPPSQPHP 218
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47605755   149 LDLSKLHET----LRTHTRLVSLFNTTLTGLHEVSAQNPTNCWICLPLNFRPYVSIPVPeqwNNFSTEINTTSVLVGPLV 224
Cdd:pfam00429 219 LAPPLPRPTsppgPGTGDRLLDLLQGAYLTLNATNPSLTQDCWLCLVSGPPYYEGIAPN---GSVSNHTSAPACSLGPQL 295
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47605755   225 SnLEITHTSNLTC---------VKFSNTTYTTNSqcirwvtpPTQIVCLPSGIFFVCGTSAYRC-----LNGSSESmCFL 290
Cdd:pfam00429 296 A-LTLSEVTGQGCciggipvghQALCNTTVSTSS--------GSHYLCAPNGTVWACGTGLTPClstalLNNTTDY-CVL 365
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47605755   291 SFLVPPMTIYTEQDLYSYVISKPRNKRVPI----LPFVIGAGVLGALGTGIGGITtSTQFYYKLSQELNGDMERVADSLV 366
Cdd:pfam00429 366 AELLPDISYHPGEPIYAIDEPAGRFRREPValtlALLLGGLGIAAGVGTGTTGLV-STQQFTSLQHALISDIQALESSIN 444
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47605755   367 TLQDQLNSLAAVVLQNRRALDLLTAERGGTCLFLGEECCYYVNQSGIVTEKVKEIRDRIQRRAEELR-NTGPWGLLSQWM 445
Cdd:pfam00429 445 DLEDSLTSLAEVVLQNRRGLDLLFLEQGGLCAALQEECCFYADHSGIVRDSIAKLQERLPQRQRLLTdNQLWFEGLFGLS 524
                         490       500       510
                  ....*....|....*....|....*....|....*.
gi 47605755   446 PWILPFL----GPLAAIILLLLFGPCIFNLLVNFVS 477
Cdd:pfam00429 525 PWFTTLLstimGPLLLLLLILLFGPCILNRLVQFIK 560
 
Name Accession Description Interval E-value
TLV_coat pfam00429
ENV polyprotein (coat polyprotein);
22-477 1.83e-55

ENV polyprotein (coat polyprotein);


Pssm-ID: 306850  Cd Length: 560  Bit Score: 195.40  E-value: 1.83e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47605755    22 PPPCRCMTSSSPYQEFLWRMQRPGNIDAPSYRSL----SKGTPTFTA-HTHMPRNCYHSATLCMHANTHYWTGK------ 90
Cdd:pfam00429  62 CSGCPDLSAYLTDQSLWPPCVTPPKRTPHANGSFyvcpGECRTRANRrHCGGYSSCYCCSWGCETTGCTYWTPAsswdyi 141
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47605755    91 ----------------------MINPSCPGGLGVTVCWTyftQTGMSDGGGVQDQAREKHVKEVISQLTRVHGTSSPYKG 148
Cdd:pfam00429 142 tvswnktsstvnctqegscnplILHFTDCGKKATTLTWG---LRLYVSGYDPLDTFRIRLKITTLNEVLRDQKPPSQPHP 218
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47605755   149 LDLSKLHET----LRTHTRLVSLFNTTLTGLHEVSAQNPTNCWICLPLNFRPYVSIPVPeqwNNFSTEINTTSVLVGPLV 224
Cdd:pfam00429 219 LAPPLPRPTsppgPGTGDRLLDLLQGAYLTLNATNPSLTQDCWLCLVSGPPYYEGIAPN---GSVSNHTSAPACSLGPQL 295
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47605755   225 SnLEITHTSNLTC---------VKFSNTTYTTNSqcirwvtpPTQIVCLPSGIFFVCGTSAYRC-----LNGSSESmCFL 290
Cdd:pfam00429 296 A-LTLSEVTGQGCciggipvghQALCNTTVSTSS--------GSHYLCAPNGTVWACGTGLTPClstalLNNTTDY-CVL 365
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47605755   291 SFLVPPMTIYTEQDLYSYVISKPRNKRVPI----LPFVIGAGVLGALGTGIGGITtSTQFYYKLSQELNGDMERVADSLV 366
Cdd:pfam00429 366 AELLPDISYHPGEPIYAIDEPAGRFRREPValtlALLLGGLGIAAGVGTGTTGLV-STQQFTSLQHALISDIQALESSIN 444
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47605755   367 TLQDQLNSLAAVVLQNRRALDLLTAERGGTCLFLGEECCYYVNQSGIVTEKVKEIRDRIQRRAEELR-NTGPWGLLSQWM 445
Cdd:pfam00429 445 DLEDSLTSLAEVVLQNRRGLDLLFLEQGGLCAALQEECCFYADHSGIVRDSIAKLQERLPQRQRLLTdNQLWFEGLFGLS 524
                         490       500       510
                  ....*....|....*....|....*....|....*.
gi 47605755   446 PWILPFL----GPLAAIILLLLFGPCIFNLLVNFVS 477
Cdd:pfam00429 525 PWFTTLLstimGPLLLLLLILLFGPCILNRLVQFIK 560
HTLV-1-like_HR1-HR2 cd09851
heptad repeat 1-heptad repeat 2 region (ectodomain) of the transmembrane subunit of human ...
345-422 7.57e-39

heptad repeat 1-heptad repeat 2 region (ectodomain) of the transmembrane subunit of human T-cell leukemia virus type 1 (HTLV-1), and related domains; This domain subfamily spans both heptad repeats of the glycoprotein (gp)/transmembrane(TM) subunit of various endogenous retroviruses (ERVs) and infectious retroviruses, including HTLV-1, HTLV -2, primate Mason-Pfizer monkey virus, Moloney murine leukemia virus, simian T-cell lymphotropic virus, feline leukemia virus (FeLV), bovine leukemia virus, and various human endogenous retroviruses (HERVs), including, HERV-H1_c2q24.3, HERV-H2_3q26, HERV-F(c)1_cXq21.33, HERV-T_19q13.11, Syncytin-1 (HERV-W_c7q21.2/ ERVWE1), Syncytin-2 (HERV-FRD_6p24.1), and related domains. This domain includes an N-terminal heptad repeat, a CKS17-like immunosuppressive region, a CX6C motif that forms an intrasubunit disulfide bond, and a C-terminal heptad repeat. N-terminal to HR1-HR2 region is a fusion peptide (FP), and C-terminal, is a membrane-spanning region (MSR). Viral infection involves the formation of a trimer-of-hairpins structure (three HR1s helices, buttressed by three HR2 helices lying in antiparallel orientation). In this structure, the FP (inserted in the host cell membrane) and MSR (inserted in the viral membrane) are in close proximity. ERVs are likely to originate from ancient germ-line infections by active retroviruses. Some modern ERVs, those that integrated into the host genome post-speciation, have a currently active exogenous counterpart, such as FeLV. Some ERVs play specific roles in the host, including placental development, protection of the host from infection by related pathogenic and exogenous retroviruses, and genome plasticity. Syncytin-1 and Syncytin-2 are expressed in the placenta, and are fusogenic, although they have a different cell specificity for fusion. Syncytin-2, but not Syncytin-1, is immunosuppressive; its immunosuppressive domain may protect the fetus from the mother's immune system. Syncytin-1 may participate in the formation of the placental trophoblast; it is also implicated in cell fusions between cancer and host cells and between cancer cell, and in human osteclast fusion. This subfamily also contains a mouse envelope protein encoded by the Fv-4 env gene, that blocks infection by exogenous MuLV.


Pssm-ID: 197368 [Multi-domain]  Cd Length: 78  Bit Score: 136.60  E-value: 7.57e-39
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 47605755 345 QFYYKLSQELNGDMERVADSLVTLQDQLNSLAAVVLQNRRALDLLTAERGGTCLFLGEECCYYVNQSGIVTEKVKEIR 422
Cdd:cd09851   1 QSYKSLSHALDADIQRLAQSISKLQKQLTSLAEVVLQNRRGLDLLTLEQGGLCAALQEECCFYANQSGLVRDSIAKLR 78
 
Name Accession Description Interval E-value
TLV_coat pfam00429
ENV polyprotein (coat polyprotein);
22-477 1.83e-55

ENV polyprotein (coat polyprotein);


Pssm-ID: 306850  Cd Length: 560  Bit Score: 195.40  E-value: 1.83e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47605755    22 PPPCRCMTSSSPYQEFLWRMQRPGNIDAPSYRSL----SKGTPTFTA-HTHMPRNCYHSATLCMHANTHYWTGK------ 90
Cdd:pfam00429  62 CSGCPDLSAYLTDQSLWPPCVTPPKRTPHANGSFyvcpGECRTRANRrHCGGYSSCYCCSWGCETTGCTYWTPAsswdyi 141
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47605755    91 ----------------------MINPSCPGGLGVTVCWTyftQTGMSDGGGVQDQAREKHVKEVISQLTRVHGTSSPYKG 148
Cdd:pfam00429 142 tvswnktsstvnctqegscnplILHFTDCGKKATTLTWG---LRLYVSGYDPLDTFRIRLKITTLNEVLRDQKPPSQPHP 218
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47605755   149 LDLSKLHET----LRTHTRLVSLFNTTLTGLHEVSAQNPTNCWICLPLNFRPYVSIPVPeqwNNFSTEINTTSVLVGPLV 224
Cdd:pfam00429 219 LAPPLPRPTsppgPGTGDRLLDLLQGAYLTLNATNPSLTQDCWLCLVSGPPYYEGIAPN---GSVSNHTSAPACSLGPQL 295
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47605755   225 SnLEITHTSNLTC---------VKFSNTTYTTNSqcirwvtpPTQIVCLPSGIFFVCGTSAYRC-----LNGSSESmCFL 290
Cdd:pfam00429 296 A-LTLSEVTGQGCciggipvghQALCNTTVSTSS--------GSHYLCAPNGTVWACGTGLTPClstalLNNTTDY-CVL 365
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47605755   291 SFLVPPMTIYTEQDLYSYVISKPRNKRVPI----LPFVIGAGVLGALGTGIGGITtSTQFYYKLSQELNGDMERVADSLV 366
Cdd:pfam00429 366 AELLPDISYHPGEPIYAIDEPAGRFRREPValtlALLLGGLGIAAGVGTGTTGLV-STQQFTSLQHALISDIQALESSIN 444
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47605755   367 TLQDQLNSLAAVVLQNRRALDLLTAERGGTCLFLGEECCYYVNQSGIVTEKVKEIRDRIQRRAEELR-NTGPWGLLSQWM 445
Cdd:pfam00429 445 DLEDSLTSLAEVVLQNRRGLDLLFLEQGGLCAALQEECCFYADHSGIVRDSIAKLQERLPQRQRLLTdNQLWFEGLFGLS 524
                         490       500       510
                  ....*....|....*....|....*....|....*.
gi 47605755   446 PWILPFL----GPLAAIILLLLFGPCIFNLLVNFVS 477
Cdd:pfam00429 525 PWFTTLLstimGPLLLLLLILLFGPCILNRLVQFIK 560
HTLV-1-like_HR1-HR2 cd09851
heptad repeat 1-heptad repeat 2 region (ectodomain) of the transmembrane subunit of human ...
345-422 7.57e-39

heptad repeat 1-heptad repeat 2 region (ectodomain) of the transmembrane subunit of human T-cell leukemia virus type 1 (HTLV-1), and related domains; This domain subfamily spans both heptad repeats of the glycoprotein (gp)/transmembrane(TM) subunit of various endogenous retroviruses (ERVs) and infectious retroviruses, including HTLV-1, HTLV -2, primate Mason-Pfizer monkey virus, Moloney murine leukemia virus, simian T-cell lymphotropic virus, feline leukemia virus (FeLV), bovine leukemia virus, and various human endogenous retroviruses (HERVs), including, HERV-H1_c2q24.3, HERV-H2_3q26, HERV-F(c)1_cXq21.33, HERV-T_19q13.11, Syncytin-1 (HERV-W_c7q21.2/ ERVWE1), Syncytin-2 (HERV-FRD_6p24.1), and related domains. This domain includes an N-terminal heptad repeat, a CKS17-like immunosuppressive region, a CX6C motif that forms an intrasubunit disulfide bond, and a C-terminal heptad repeat. N-terminal to HR1-HR2 region is a fusion peptide (FP), and C-terminal, is a membrane-spanning region (MSR). Viral infection involves the formation of a trimer-of-hairpins structure (three HR1s helices, buttressed by three HR2 helices lying in antiparallel orientation). In this structure, the FP (inserted in the host cell membrane) and MSR (inserted in the viral membrane) are in close proximity. ERVs are likely to originate from ancient germ-line infections by active retroviruses. Some modern ERVs, those that integrated into the host genome post-speciation, have a currently active exogenous counterpart, such as FeLV. Some ERVs play specific roles in the host, including placental development, protection of the host from infection by related pathogenic and exogenous retroviruses, and genome plasticity. Syncytin-1 and Syncytin-2 are expressed in the placenta, and are fusogenic, although they have a different cell specificity for fusion. Syncytin-2, but not Syncytin-1, is immunosuppressive; its immunosuppressive domain may protect the fetus from the mother's immune system. Syncytin-1 may participate in the formation of the placental trophoblast; it is also implicated in cell fusions between cancer and host cells and between cancer cell, and in human osteclast fusion. This subfamily also contains a mouse envelope protein encoded by the Fv-4 env gene, that blocks infection by exogenous MuLV.


Pssm-ID: 197368 [Multi-domain]  Cd Length: 78  Bit Score: 136.60  E-value: 7.57e-39
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 47605755 345 QFYYKLSQELNGDMERVADSLVTLQDQLNSLAAVVLQNRRALDLLTAERGGTCLFLGEECCYYVNQSGIVTEKVKEIR 422
Cdd:cd09851   1 QSYKSLSHALDADIQRLAQSISKLQKQLTSLAEVVLQNRRGLDLLTLEQGGLCAALQEECCFYANQSGLVRDSIAKLR 78
ENVV1-like_HR1-HR2 cd09950
heptad repeat 1-heptad repeat 2 region (ectodomain) of the transmembrane subunit of the human ...
363-424 3.78e-17

heptad repeat 1-heptad repeat 2 region (ectodomain) of the transmembrane subunit of the human endogenous retrovirus ENVV1, and related domains; This domain subfamily spans both heptad repeats of the glycoprotein (gp)/transmembrane subunit of various endogenous retroviruses (ERVs), including chicken FET-1 (Female Expressed Transcript 1) protein, and the envelope proteins of the human ERVs (HERVs): ENVV1 (also known as HERV-V2_c19q13.41) and ENVV2 (also known as HERV-V1_c19q13.41 ). This domain belongs to a larger superfamily containing the HR1-HR2 domain of endogenous retroviruses (ERVs) and infectious retroviruses, such as Ebola virus, Rous sarcoma virus and human immunodeficiency virus type 1. This domain includes an N-terminal heptad repeat, a CKS17-like immunosuppressive region, a CX6C motif that forms an intra-subunit disulfide bond, and a C-terminal heptad repeat. N-terminal to HR1-HR2 region is a fusion peptide (FP), and C-terminal, is a membrane-spanning region (MSR). Viral infection involves the formation of a trimer-of-hairpins structure (three HR1 helices, buttressed by three HR2 helices lying in antiparallel orientation). In this structure, the FP (inserted in the host cell membrane) and MSR (inserted in the viral membrane) are in close proximity. ERVs are likely to originate from ancient germ-line infections by active retroviruses. Some ERVs play specific roles in the host, including placental development, protection of the host from infection by related pathogenic and exogenous retroviruses, and genome plasticity. FET-1 may have an ovary-determining role. The FET-1 gene is located on the female specific W chromosome in chickens. During the sex-determining period, the FET-1 transcript is up-regulated in the cortex of the left gonad (the only gonad which develops in female chickens); it is also expressed at a lower level, in neural tissue and waste collection ducts. The genes encoding ENVV1 and ENVV2 proteins are located in tandem on chromosome 19q13.41, and show placenta-specific expression in human and baboon.


Pssm-ID: 197373 [Multi-domain]  Cd Length: 72  Bit Score: 76.09  E-value: 3.78e-17
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 47605755 363 DSLVTLQDQLNSLAAVVLQNRRALDLLTAERGGTCLFLGEECCYYVNQSGIVTEKVKEIRDR 424
Cdd:cd09950  11 DSISALQAEVSSLSNVVLQNRMALDLLLAEQGGVCAVINQSCCAYVNNSGRIETDIKKIYDQ 72
Ebola_RSV-like_HR1-HR2 cd09948
heptad repeat 1-heptad repeat 2 region of the transmembrane subunit of various endogenous ...
353-423 2.07e-14

heptad repeat 1-heptad repeat 2 region of the transmembrane subunit of various endogenous retroviruses (ERVs) and infectious retroviruses, including Ebola virus and Rous sarcoma virus; This domain family spans both heptad repeats of the glycoprotein (gp)/transmembrane subunit of endogenous retroviruses (ERVs) and infectious retroviruses, including Ebola virus gp2, Rous sarcoma virus gp37, and the envelope proteins of various ERVs. This domain includes an N-terminal heptad repeat, a CKS17-like immunosuppressive region, a CX6C motif that forms an intra-subunit disulfide bond, and a C-terminal heptad repeat. N-terminal to HR1-HR2 region is a fusion peptide (FP), while C-terminal, is a membrane-spanning region (MSR). Viral infection involves the formation of a trimer-of-hairpins structure (three HR1s helices, buttressed by three HR2 helices lying in antiparallel orientation). In this structure, the FP (inserted in the host cell membrane) and MSR (inserted in the viral membrane) are in close proximity. ERVs are likely to originate from ancient germ-line infections by active retroviruses. Some modern ERVs, those that integrated into the host genome post-speciation, have a currently active exogenous counterpart, such as Jaagsiekte sheep retrovirus (JSRV), feline leukemia virus (FeLV), and avian leukemia virus (ALV). Some ERVs play specific roles in the host, including placental development, protection of the host from infection by related pathogenic and exogenous retroviruses, and genome plasticity. Human ERVs (HERVs) belonging to this family include Syncytin-1 (HERV-W_c7q21.2/ ERVWE1), and Syncytin-2 (HERV-FRD_6p24.1) which are expressed in the placenta, and are fusogenic, although they have a different cell specificity for fusion. Syncytin-2, but not Syncytin-1, is immunosuppressive. Its immunosuppressive domain may protect the fetus from the mother's immune system. Syncytin-1 may participate in the formation of the placental trophoblast. It is also implicated in cell fusions between cancer and host cells and between cancer cells, and in human osteclast fusion. This family also contains human HERV-R_c7q21.2 (ERV-3), which is also expressed in the placenta, but is not fusogenic, has an immunosuppressive domain, but lacks a fusion peptide. It is unclear whether ERV-3 has a critical biological role.


Pssm-ID: 197371 [Multi-domain]  Cd Length: 72  Bit Score: 68.26  E-value: 2.07e-14
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 47605755 353 ELNGDMERVADSLVTLQDQLNSLAAVVLQNRRALDLLTAERGGTCLFLGEECCYYVN-QSGIVTEKVKEIRD 423
Cdd:cd09948   1 GLEQDANETTQALQLFLRNVTSLRTVVLQNRRALDFLLAREGGTCHIINEDCCCFLNdQSRITDKIDQLIEQ 72
HERV-Rb-like_HR1-HR2 cd09951
heptad repeat 1- heptad repeat 2 region (ectodomain) of the transmembrane subunit of the human ...
363-408 8.67e-09

heptad repeat 1- heptad repeat 2 region (ectodomain) of the transmembrane subunit of the human endogenous retrovirus HERV-R(b)_c3p24.3 and related domains; This domain subfamily spans both heptad repeats of the glycoprotein (gp)/transmembrane subunit of various endogenous retroviruses (ERVs) including the human ERVs (HERVs): HERV-R(b)_c3p24.3 and Syncytin-3 (also known as HERV-P(b)_c14q32.12). This domain belongs to a larger superfamily containing the HR1-HR2 domain of endogenous retroviruses (ERVs) and infectious retroviruses, such as Ebola virus, Rous sarcoma virus (RSV) and human immunodeficiency virus type 1 (HIV-1). This domain includes an N-terminal heptad repeat, a CKS17-like immunosuppressive region, a CX6C motif that forms an intrasubunit disulfide bond, and a C-terminal, is a heptad repeat. In intact retroviruses, N-terminal to HR1-HR2 region is a fusion peptide (FP), and C-terminal, is a membrane-spanning region (MSR). Viral infection involves the formation of a trimer-of-hairpins structure (three HR1s helices, buttressed by three HR2 helices lying in antiparallel orientation). In this structure, the FP (inserted in the host cell membrane) and MSR (inserted in the viral membrane) are in close proximity. ERVs are likely to originate from ancient germ-line infections by active retroviruses. Some ERVs play specific roles in the host, including placental development, protection of the host from infection by related pathogenic and exogenous retroviruses, and genome plasticity. Syncytin-3 is fusogenic, HERV-R(b)_c3p24.3 appears not to have fusogenic activity.


Pssm-ID: 197374  Cd Length: 81  Bit Score: 52.56  E-value: 8.67e-09
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 47605755 363 DSLVTLQDQLNSLAAVVLQNRRALDLLTAERGGTCLFLGEECCYYV 408
Cdd:cd09951  15 QAISGMNEQLYATSLMALQNRMALDMLLAEKGGVCSMIKTECCTYI 60
Ebola_HIV-1-like_HR1-HR2 cd09947
heptad repeat 1-heptad repeat 2 region (ectodomain) of the transmembrane subunit of various ...
353-424 1.36e-07

heptad repeat 1-heptad repeat 2 region (ectodomain) of the transmembrane subunit of various endogenous retroviruses (ERVs) and infectious retroviruses, including Ebola virus and human immunodeficiency virus type 1 (HIV-1); This domain superfamily spans both heptad repeats of the glycoprotein (gp)/transmembrane subunit of various endogenous retroviruses (ERVs) and infectious retroviruses, including Ebola virus gp2, Rous sarcoma virus gp37, human immunodeficiency virus type 1 (HIV-1) gp41, and the envelope proteins of various ERVs. In the HR1-HR2 region of Ebola virus and RSV, the linker region between the two repeats includes a CKS17-like immunosuppressive region and a CX6C motif that forms an intra-subunit disulfide bond; MMTV, HIV-1, HERV-K endogenous retroviruses and related sequences lack a canonical CSK17-like sequence, and CX6C motif. N-terminal to the HR1-HR2 region is a fusion peptide (FP), and C-terminal, is a membrane-spanning region (MSR). Viral infection involves the formation of a trimer-of-hairpins structure (three HR1 helices, buttressed by three HR2 helices lying in antiparallel orientation). In this structure, the FP (inserted in the host cell membrane) and MSR (inserted in the viral membrane) are in close proximity. ERVs are likely to originate from ancient germ-line infections by active retroviruses. Some modern ERVs, those that integrated into the host genome post-speciation, have a currently active exogenous counterpart, such as Jaagsiekte sheep retrovirus (JSRV), feline leukemia virus (FeLV), and avian leukemia virus (ALV). Some ERVs play specific roles in the host, including placental development, protection of the host from infection by related pathogenic and exogenous retroviruses, and genome plasticity. Human ERVs (HERVs) belonging to this superfamily include Syncytin-1 (HERV-W_c7q21.2/ ERVWE1), and Syncytin-2 (HERV-FRD_6p24.1) which are expressed in the placenta, and are fusogenic, although they have a different cell specificity for fusion. Syncytin-2, but not Syncytin-1, is immunosuppressive; its immunosuppressive domain may protect the fetus from the mother's immune system. Syncytin-1 may participate in the formation of the placental trophoblast; it is also implicated in cell fusions between cancer and host cells and between cancer cell, and in human osteclast fusion. This superfamily also contains human HERV-R_c7q21.2 (ERV-3), which is also expressed in the placenta, but is not fusogenic, and has an immunosuppressive domain, but lacks a fusion peptide. It is unclear whether ERV-3 has a critical biological role. Included in this superfamily are ERVs from domestic sheep that are related to JSRV, the agent of transmissible lung cancer in sheep; for example, enJSRV-26 that retains an intact genome. These endogenous JSRVs protect the sheep against JSRV infection and are required for sheep placental development.


Pssm-ID: 197370  Cd Length: 73  Bit Score: 48.76  E-value: 1.36e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 47605755 353 ELNGDMERVADSLVTLQDQLNSLAAVVLQNRRALDLLTAERGGTCLFLGEECCYYVN-QSGIVTEKVKEIRDR 424
Cdd:cd09947   1 RLQQLLRLTTQAIKNLHTNLTAIAKYLAQNRRGLDWLAARRGGTCVALTEVCCPFLSiTNKWWQDWIRKLDFL 73
Ebola-like_HR1-HR2 cd09850
heptad repeat 1-heptad repeat 2 region of the transmembrane subunit of Filoviridae viruses, ...
362-429 2.60e-07

heptad repeat 1-heptad repeat 2 region of the transmembrane subunit of Filoviridae viruses, Ebola virus and Marburg virus, and related domains; This domain subfamily spans both heptad repeats of the glycoprotein (gp)/transmembrane subunit of various endogenous retroviruses (ERVs) and infectious retroviruses, including Ebola virus gp2, Marburg virus gp, and the envelope proteins of various ERVs, including human HERV-R_c7q21.2 (ERV-3). This domain includes an N-terminal heptad repeat, a CKS17-like immunosuppressive region, a CX6C motif that forms an intrasubunit disulfide bond, and a C-terminal heptad repeat. N-terminal to HR1-HR2 region is a fusion peptide (FP), and C-terminal, is a membrane-spanning region (MSR). Viral infection involves the formation of a trimer-of-hairpins structure (three HR1s helices, buttressed by three HR2 helices lying in antiparallel orientation). In this structure, the FP (inserted in the host cell membrane) and MSR (inserted in the viral membrane) are in close proximity. ERVs are likely to originate from ancient germ-line infections by active retroviruses. Some ERVs play specific roles in the host. However, it is unclear whether ERV-3 has a critical biological role: it is expressed in the placenta, but is not fusogenic, has an immunosuppressive domain, but lacks a fusion peptide. Filoviridae, the family of viruses including Ebola and Marburg, may have acquired this domain via horizontal transfer from retroviruses.


Pssm-ID: 197367  Cd Length: 77  Bit Score: 48.25  E-value: 2.60e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 47605755 362 ADSLVTLQDQLNSLAAVVLQNRRALDLLTAERGGTCLFLGE-ECCYYVNQSGivtEKVKEIRDRIQRRA 429
Cdd:cd09850  10 AQALELLLRQTTEMRTFSYQNRLALDYLLAREGGVCGKFNPdNCCIEIDDWG---EVIKNITDKIDQIA 75
IgC2_CD33_d2_like cd20987
Second immunoglobulin domain of Cluster of Differentiation (CD) 33 and related Siglecs; member ...
177-248 5.61e-03

Second immunoglobulin domain of Cluster of Differentiation (CD) 33 and related Siglecs; member of the C2-set of IgSF domains; The members here are composed of the second immunoglobulin (Ig) domain of Cluster of Differentiation (CD) 33 (also known as sialic-acid binding immunoglobulin type-lectin 3 (Siglec-3)) and related Siglecs. CD33, a Siglec family member, is a well-known immunotherapeutic target in acute myeloid leukemia (AML). It is an inhibitory sialoadhesin expressed in human leukocytes of the myeloid lineage and some lymphoid subsets, including natural killer (NK) cells. Siglecs are primarily expressed on immune cells and recognize sialic acid-containing glycan ligands. Siglecs are organized as an extracellular module composed of Ig-like domains (an N-terminal variable set of Ig-like carbohydrate recognition domains, and 1 to 16 constant Ig-like domains), followed by transmembrane and short cytoplasmic domains. Human Siglecs are classified into two subgroups, one subgroup is comprised of sialoadhesin (Siglec-1), CD22 (Siglec-2), and MAG (Siglec-4, myelin-associated glycoprotein), the other subgroup is comprised of CD33-related Siglecs which include CD33 (Siglec-3) and human Siglecs 5-11. CD33 (Siglec-3) is the smallest Siglec member. It preferentially binds to alpha2-6- and alpha2-3-sialylated glycans and strongly binds to sialylated ligands on leukemic cell lines. Ig Superfamily (IgSF) domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. This group includes CD33-related Siglecs which belong to the C2-set of IgSF domains. Unlike the C1-set, the C2-set structures do not have a D strand.


Pssm-ID: 409579  Cd Length: 94  Bit Score: 36.39  E-value: 5.61e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 47605755 177 EVSAQNPTNCwICLPLNFRPYVSIPVPEQWNNFSTEINTTSVLVgplvSNLEIT-----HTSNLTC-VKFSNTTYTTN 248
Cdd:cd20987  16 TLTCSVPDNC-PALSPEFSWLGAALTPLPPVLGRLEEEGTTTHS----SVLTFTprpedHGTNLTCqVKFPGATVTTE 88
 
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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