8BGG
Cryo-EM structure of SARS-CoV-2 spike (Omicron BA.1 variant) in complex with nanobody W25 (map 5, focus refinement on RBD, W25 and adjacent NTD)
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| B | 0016020 | cellular_component | membrane |
| B | 0019031 | cellular_component | viral envelope |
| B | 0019064 | biological_process | fusion of virus membrane with host plasma membrane |
| B | 0039654 | biological_process | fusion of virus membrane with host endosome membrane |
| B | 0046813 | biological_process | receptor-mediated virion attachment to host cell |
| B | 0055036 | cellular_component | virion membrane |
| B | 0075509 | biological_process | endocytosis involved in viral entry into host cell |
| C | 0016020 | cellular_component | membrane |
| C | 0019031 | cellular_component | viral envelope |
| C | 0019064 | biological_process | fusion of virus membrane with host plasma membrane |
| C | 0039654 | biological_process | fusion of virus membrane with host endosome membrane |
| C | 0046813 | biological_process | receptor-mediated virion attachment to host cell |
| C | 0055036 | cellular_component | virion membrane |
| C | 0075509 | biological_process | endocytosis involved in viral entry into host cell |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 2 |
| Details | SITE: Cleavage; by host furin => ECO:0000255|HAMAP-Rule:MF_04099, ECO:0000269|PubMed:32142651, ECO:0000269|PubMed:32362314, ECO:0000269|PubMed:32703818, ECO:0000269|PubMed:34159616 |
| Chain | Residue | Details |
| B | SER685 | |
| C | SER685 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 2 |
| Details | SITE: Cleavage; by host TMPRSS2 or CTSL => ECO:0000255|HAMAP-Rule:MF_04099, ECO:0000269|PubMed:32703818, ECO:0000269|PubMed:34159616 |
| Chain | Residue | Details |
| B | ARG815 | |
| C | ARG815 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 6 |
| Details | CARBOHYD: N-linked (GlcNAc...) (complex) asparagine; by host => ECO:0000255|HAMAP-Rule:MF_04099, ECO:0000269|PubMed:32366695, ECO:0000269|PubMed:32979942 |
| Chain | Residue | Details |
| B | ASN17 | |
| B | ASN1158 | |
| B | ASN1173 | |
| C | ASN20 | |
| C | ASN1158 | |
| C | ASN1173 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 10 |
| Details | CARBOHYD: N-linked (GlcNAc...) (hybrid) asparagine; by host => ECO:0000255|HAMAP-Rule:MF_04099, ECO:0000269|PubMed:32155444, ECO:0000269|PubMed:32363391, ECO:0000269|PubMed:32366695, ECO:0000269|PubMed:32979942 |
| Chain | Residue | Details |
| B | ASN61 | |
| C | ASN1074 | |
| B | THR124 | |
| B | ASN717 | |
| B | ASN801 | |
| B | ASN1074 | |
| C | ASN64 | |
| C | THR125 | |
| C | ASN717 | |
| C | ASN801 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 6 |
| Details | CARBOHYD: N-linked (GlcNAc...) (complex) asparagine; by host => ECO:0000255|HAMAP-Rule:MF_04099, ECO:0000269|PubMed:32363391, ECO:0000269|PubMed:32366695, ECO:0000269|PubMed:32979942 |
| Chain | Residue | Details |
| B | THR76 | |
| B | GLU154 | |
| B | ASN1194 | |
| C | THR77 | |
| C | GLU152 | |
| C | ASN1194 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 14 |
| Details | CARBOHYD: N-linked (GlcNAc...) (complex) asparagine; by host => ECO:0000255|HAMAP-Rule:MF_04099, ECO:0000269|PubMed:32155444, ECO:0000269|PubMed:32363391, ECO:0000269|PubMed:32366695, ECO:0000269|PubMed:32979942 |
| Chain | Residue | Details |
| B | TYR170 | |
| C | ASN331 | |
| C | ASN343 | |
| C | ASN616 | |
| C | ASN657 | |
| C | ASN1098 | |
| B | ASN282 | |
| B | ASN331 | |
| B | ASN343 | |
| B | ASN616 | |
| B | ASN657 | |
| B | ASN1098 | |
| C | TYR168 | |
| C | ASN282 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 4 |
| Details | CARBOHYD: N-linked (GlcNAc...) (high mannose) asparagine; by host => ECO:0000255|HAMAP-Rule:MF_04099, ECO:0000269|PubMed:32155444, ECO:0000269|PubMed:32363391, ECO:0000269|PubMed:32366695, ECO:0000269|PubMed:32979942 |
| Chain | Residue | Details |
| B | ASN236 | |
| B | ASN709 | |
| C | ASN234 | |
| C | ASN709 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 2 |
| Details | CARBOHYD: O-linked (GalNAc) threonine; by host => ECO:0000269|PubMed:32363391 |
| Chain | Residue | Details |
| B | THR323 | |
| C | THR323 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 2 |
| Details | CARBOHYD: O-linked (HexNAc...) serine; by host => ECO:0000269|PubMed:32363391 |
| Chain | Residue | Details |
| B | SER325 | |
| C | SER325 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 2 |
| Details | CARBOHYD: N-linked (GlcNAc...) (hybrid) asparagine; by host => ECO:0000255|HAMAP-Rule:MF_04099, ECO:0000269|PubMed:32155444, ECO:0000269|PubMed:32366695, ECO:0000269|PubMed:32979942 |
| Chain | Residue | Details |
| B | ASN603 | |
| C | ASN603 |
| site_id | SWS_FT_FI11 |
| Number of Residues | 4 |
| Details | CARBOHYD: O-linked (GlcNAc...) threonine; by host GALNT1 => ECO:0000269|PubMed:34732583 |
| Chain | Residue | Details |
| B | THR676 | |
| B | THR678 | |
| C | THR676 | |
| C | THR678 |
| site_id | SWS_FT_FI12 |
| Number of Residues | 2 |
| Details | CARBOHYD: N-linked (GlcNAc...) (complex) asparagine; by host => ECO:0000255|HAMAP-Rule:MF_04099, ECO:0000269|PubMed:32155444, ECO:0000269|PubMed:32366695, ECO:0000269|PubMed:32979942 |
| Chain | Residue | Details |
| B | ASN1134 | |
| C | ASN1134 |
