9YTC
Cryo-EM structure of SARS-CoV-2 Omicron neutralizing antibody S212 with BA.5 RBD and SP1-77 Fab complex
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A (A) | Spike glycoprotein | polymer | 676 | 75811.5 | 1 | UniProt (P0DTC2) | Severe acute respiratory syndrome coronavirus (2019-nCoV SARS-CoV-2) | S glycoprotein,E2,Peplomer protein |
| 2 | B (D) | SP1-77 Fab heavy chain | polymer | 451 | 49665.7 | 1 | Mus musculus (mouse) | ||
| 3 | C (E) | SP1-77 Fab light chain | polymer | 213 | 23294.6 | 1 | Mus musculus (mouse) | ||
| 4 | D (F) | S212 Fab heavy chain | polymer | 449 | 49558.7 | 1 | Mus musculus (mouse) | ||
| 5 | E (G) | S212 Fab light chain | polymer | 214 | 23535.0 | 1 | Mus musculus (mouse) | ||
| 6 | F (T) | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 570.5 | 1 | In PDB | |||
| 7 | G (A) | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 1 | Chemie (NAG) |
Sequence modifications
A: 7 - 673 (UniProt: P0DTC2)
| PDB | External Database | Details |
|---|---|---|
| Met -2 | - | initiating methionine |
| Phe -1 | - | expression tag |
| Leu 0 | - | expression tag |
| Leu 1 | - | expression tag |
| Thr 2 | - | expression tag |
| Thr 3 | - | expression tag |
| Lys 4 | - | expression tag |
| Arg 5 | - | expression tag |
| Thr 6 | - | expression tag |
| Ile 25 | Thr 19 | conflict |
| - | Leu 24 | deletion |
| - | Pro 25 | deletion |
| - | Pro 26 | deletion |
| Ser 30 | Ala 27 | conflict |
| - | His 69 | deletion |
| - | Val 70 | deletion |
| Asp 143 | Gly 142 | conflict |
| - | Tyr 144 | deletion |
| Gly 213 | Val 213 | conflict |
| Asp 339 | Gly 339 | conflict |
| Phe 371 | Ser 371 | conflict |
| Pro 373 | Ser 373 | conflict |
| Phe 375 | Ser 375 | conflict |
| Ala 376 | Thr 376 | conflict |
| Asn 405 | Asp 405 | conflict |
| Ser 408 | Arg 408 | conflict |
| Asn 417 | Lys 417 | conflict |
| Arg 452 | Leu 452 | conflict |
| Asn 477 | Ser 477 | conflict |
| Lys 478 | Thr 478 | conflict |
| Ala 484 | Glu 484 | conflict |
| Val 486 | Phe 486 | conflict |
| Arg 498 | Gln 498 | conflict |
| Tyr 501 | Asn 501 | conflict |
| His 505 | Tyr 505 | conflict |
| Gly 614 | Asp 614 | conflict |
| Tyr 655 | His 655 | conflict |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 5 |
| Total formula weight | 221865.4 | |
| Branched | Number of molecules | 1 |
| Total formula weight | 570.5 | |
| Non-Polymers* | Number of molecules | 1 |
| Total formula weight | 221.2 | |
| All* | Total formula weight | 222657.2 |
