9UPR
Cryo-EM structure of the N-terminal domain of Omicron BA.1 in complex with nanobody N103 and S2L20 Fab
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A (A) | S2L20 light chain | polymer | 236 | 26018.0 | 1 | Homo sapiens | ||
| 2 | B (B) | S2L20 heavy chain | polymer | 473 | 52041.5 | 1 | Homo sapiens | ||
| 3 | C (E) | nanobody N103 | polymer | 122 | 12959.4 | 1 | Vicugna pacos | ||
| 4 | D (F) | Spike glycoprotein | polymer | 306 | 34909.5 | 1 | UniProt (P0DTC2) Pfam (PF16451) | Severe acute respiratory syndrome coronavirus 2 (2019-nCoV SARS-CoV-2) | S glycoprotein,E2,Peplomer protein |
| 5 | E (C) | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 424.4 | 1 | In PDB GlyTouCan (G42666HT) | |||
| 6 | F, G, H, I (F) | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 4 | Chemie (NAG) PubChem (24139) |
Sequence modifications
F: 1 - 305 (UniProt: P0DTC2)
| PDB | External Database | Details |
|---|---|---|
| Val 67 | Ala 67 | variant |
| - | His 69 | deletion |
| - | Val 70 | deletion |
| Ile 95 | Thr 95 | variant |
| Asp 145 | Gly 142 | variant |
| - | Val 143 | deletion |
| - | Tyr 144 | deletion |
| - | Tyr 145 | deletion |
| Arg 211 | Asn 211 | conflict |
| Glu 212 | Leu 212 | conflict |
| Pro 213 | Val 213 | conflict |
| Glu 214 | Arg 214 | conflict |
| His 306 | - | expression tag |
| His 307 | - | expression tag |
| His 308 | - | expression tag |
| His 309 | - | expression tag |
| His 310 | - | expression tag |
| His 311 | - | expression tag |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 4 |
| Total formula weight | 125928.3 | |
| Branched | Number of molecules | 1 |
| Total formula weight | 424.4 | |
| Non-Polymers* | Number of molecules | 4 |
| Total formula weight | 884.8 | |
| All* | Total formula weight | 127237.5 |
