5GYQ


Conserved Protein Domain Family
bCoV_S1_RBD

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pfam09408: bCoV_S1_RBD (This model is not part of the current CDD release)
Betacoronavirus spike glycoprotein S1, receptor binding
This entry represents the receptor binding domain (S1 RBD) of the betacoronavirus spike glycoprotein. The spike glycoprotein is arranged in trimers on the surface of the viral membrane and is essential for viral entry. The spike protein is translated as a large polypeptide that is subsequently cleaved to the distal S1, responsible for receptor binding, and the membrane-anchored S2 responsible for membrane fusion. The coronavirus (SARS-CoV) S1 subunit is composed of two distinct domains: an N-terminal domain (S1 NTD) and a receptor-binding domain (S1 RBD) also referred to as the S1 CTD or domain B. Each of these domains have been implicated in binding to host receptors. However, most coronaviruses are not known to utilize both the S1 NTD and S1 RBD for viral entry. SARS-CoV makes use of its S1 RBD to bind to the human angiotensin-converting enzyme 2 (ACE2) as its host receptor.
Statistics
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PSSM-Id: 518886
Aligned: 9 rows
Threshold Bit Score: 158.053
Created: 15-Feb-2025
Updated: 28-Apr-2025
Structure
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Program:
Drawing:
Aligned Rows:
PubMed ReferencesClick to see Conserved Features Help

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
5GYQ_A         17 PQPVVWRRYMLYDCVFDFTVVVDSLPTHQLQCYGVSPRRLASMCYGSVTLDVMRINETHLNNLFNRVPDTFSLYNYALPD 96   Rousettus bat...
A3EXG6        368 PQPVVWRRYMLYDCVFDFTVVVDSLPTHQLQCYGVSPRRLASMCYGSVTLDVMRINETHLNNLFNRVPDTFSLYNYALPD 447  Rousettus bat...
2_pfamImport    1 PQPIAWRRYAVSKCGFDFEAVINRLPTFELKCFGVSPARLASMCYGKVTIDVFRINVTHLANLIAGVPDAFSKYNYALPR 80  
YP_009273005  376 PSPAAWVRATISNCTFDFESLLRTLPTYNLKCYGISPARLSTMCYAGVTLDIFKLNTTHLSNMLGSVPDAVSIYNYALPS 455 
YP_009113025  344 PSPISWERKTFSNCNFNMSSLLSKVRATSFSCNNIDASKIYDMCFGSITIDKFAIPNSRKVDLQFGSSGYIQNYNYRLDQ 423 
1_pfamImport    1 PQVYNFSRLVFTNCNYNLTKLLALFQVSQFSCHQVSPSALASGCYSSLTVDYFAYPTYMSSYLQQGSTGEISQFNYKQDF 80  
YP_009513010  382 PIIANYSRRVFTNCNYNLTKLLSLVQVDEFVCHKTTPEALATGCYSSLTVDWFALPFSMKSTLAIGSAEAISMFNYNQDY 461 
P59594        335 PSVYAWERKKISNCVADYSVLYNSTFFSTFKCYGVSATKLNDLCFSNVYADSFVVKGDDVRQIAPGQTGVIADYNYKLPD 414  Severe acute ...
YP_009072440  371 PSPAFWRRHYVRNCNYDISVFTDNADVYSLQCYGVAPSSLADMCWEEAHIDYMKISEKDIFSFKPSGAGDFAKYNYKLPS 450 
5GYQ_A         97 NFYGCLHAF-----------------YLNSTAP-YAVA---NRFP----------------------IKPGGRQ--SNSA 131  Rousettus bat...
A3EXG6        448 NFYGCLHAF-----------------YLNSTAP-YAVA---NRFP----------------------IKPGGRQ--SNSA 482  Rousettus bat...
2_pfamImport   81 DFYGCVHAF-----------------YVNMSSD-YIIA---DSWPav-------------------vIQPGGRQ--TDSS 118 
YP_009273005  456 NFYGCVHAY-----------------HLNSTTP-YAVAvppGAYP----------------------IKPGGRQ--LFNS 493 
YP_009113025  424 SATSCQLYYgipann-----vtvtkkNPSGWNNrYGFV---Efkplnigqnyn---kysaiystmcfNVPNDYC--PCKL 490 
1_pfamImport   81 SNPTCRILAtvpanlsa-----------------sgllpkpSNYVwlsecyqns-----ftgknfqyVKAGQYT--PCLG 136 
YP_009513010  462 SNPTCRIHAavtanvst-----------------alnftanANYAyisrcqg--------vdgkpilLQPGQMTniACRS 516 
P59594        415 DFMGCVLAW-----------------NTRNIDAtSTGN---YNYKyr-------------------yLRHGKLR--PFER 453  Severe acute ...
YP_009072440  451 DFMGCTVVFtnqeltcnatsgqlchvYTNNLTNyPAEAtawDKSHyesieryqmwssenvyncelqeVGPQQFNrmPRNC 530 
5GYQ_A        132 FIDTvi--nAA--HYSPFSYVYGl---------------------AVITLKPAAGSKLVCP 167  Rousettus bat coronavirus HKU9
A3EXG6        483 FIDTvi--nAA--HYSPFSYVYGl---------------------AVITLKPAAGSKLVCP 518  Rousettus bat coronavirus HKU9
2_pfamImport  119 LVGTwl--nSPakSHCTILSCFGv---------------------AVIGLQPASGTQLVCP 156 
YP_009273005  494 FVSQvl--dSPt-SQCTPANCMGv---------------------VVIGLTPASGSNLVCP 530 
YP_009113025  491 ----------------------------------------------------------GCP 493 
1_pfamImport  137 -LAAngfekSYqtHRDPVSKlavtgvvtp--------mtsalqmaFIISVQYGTDSNSVCP 188 
YP_009513010  517 GVLArpsdaDYfgYS-----FQGrnyylgrksykpktdegdvqmvYVITPKYDKGPDTVCP 572 
P59594        454 DISNvp--fSPdgKPCTPPALNCywplndygfytttgigyqpyrvVVLSFELLNAPATVCG 512  Severe acute respiratory syndrom...
YP_009072440  531 YVRS-----NNsnDYWQPMSFRGvnsl---------------mvaMAITLKPTRTSATVCG 571 
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