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)
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | B, C | Spike glycoprotein | polymer | 1205 | 133912.0 | 2 | UniProt (P0DTC2) Pfam (PF16451) Pfam (PF09408) Pfam (PF19209) Pfam (PF01601) In PDB | Severe acute respiratory syndrome coronavirus 2 | S glycoprotein,E2,Peplomer protein |
| 2 | Y | Nanobody W25 | polymer | 167 | 17827.1 | 1 | Vicugna pacos | ||
| 3 | A | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 910.8 | 1 | In PDB GlyTouCan (G22768VO) | |||
| 4 | D | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 586.5 | 1 | In PDB GlyTouCan (G15407YE) | |||
| 5 | B, C | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 5 | Chemie (NAG) |
Sequence modifications
B, C: 1 - 1207 (UniProt: P0DTC2)
| PDB | External Database | Details |
|---|---|---|
| Val 67 | Ala 67 | conflict |
| - | His 69 | deletion |
| - | Val 70 | deletion |
| Ile 95 | Thr 95 | conflict |
| - | Gly 142 | deletion |
| - | Val 143 | deletion |
| - | Tyr 144 | deletion |
| Asp 142 | Tyr 145 | conflict |
| Ile 211 | - | insertion |
| Val 212 | - | insertion |
| Arg 213 | Asn 211 | conflict |
| Glu 214 | Leu 212 | conflict |
| Pro 215 | Val 213 | conflict |
| Glu 216 | Arg 214 | conflict |
| Asp 339 | Gly 339 | conflict |
| Leu 371 | Ser 371 | conflict |
| Pro 373 | Ser 373 | conflict |
| Phe 375 | Ser 375 | conflict |
| Asn 417 | Lys 417 | conflict |
| Lys 440 | Asn 440 | conflict |
| Ser 446 | Gly 446 | conflict |
| Asn 477 | Ser 477 | conflict |
| Lys 478 | Thr 478 | conflict |
| Ala 484 | Glu 484 | conflict |
| Lys 493 | Gln 493 | conflict |
| Ser 496 | Gly 496 | conflict |
| Arg 498 | Gln 498 | conflict |
| Tyr 501 | Asn 501 | conflict |
| His 505 | Tyr 505 | conflict |
| Lys 547 | Thr 547 | conflict |
| Gly 614 | Asp 614 | conflict |
| Tyr 655 | His 655 | conflict |
| Lys 679 | Asn 679 | conflict |
| His 681 | Pro 681 | conflict |
| Gly 682 | Arg 682 | conflict |
| Ser 683 | Arg 683 | conflict |
| Ser 685 | Arg 685 | conflict |
| Lys 764 | Asn 764 | conflict |
| Tyr 796 | Asp 796 | conflict |
| Pro 817 | Phe 817 | conflict |
| Lys 856 | Asn 856 | conflict |
| Pro 892 | Ala 892 | conflict |
| Pro 899 | Ala 899 | conflict |
| Pro 942 | Ala 942 | conflict |
| His 954 | Gln 954 | conflict |
| Lys 969 | Asn 969 | conflict |
| Phe 981 | Leu 981 | conflict |
| Pro 986 | Lys 986 | conflict |
| Pro 987 | Val 987 | conflict |
| Gln 1208 | - | expression tag |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 3 |
| Total formula weight | 285651.2 | |
| Branched | Number of molecules | 2 |
| Total formula weight | 1497.4 | |
| Non-Polymers* | Number of molecules | 5 |
| Total formula weight | 1106.0 | |
| All* | Total formula weight | 288254.6 |
